The ChEMBL-og

A recurring thing we are interested in is classifying the natural ligand/partner of a protein. Having a classification of the 'natural' ligand partner for every human protein would be really useful, and would allow us to ask and more importantly answer quite complex questions in ChEMBL like - ' show me all small molecules that modulate a protein-protein interaction (PPI) at better than 100 nM potency? '. I've had a bit of a dig around the web, but there isn't anything that does exactly what I need (or I'm not smart enough to find it), but I'm sure it must exist, so in the comments section, please post resources and ideas.....

ATC code (partial): J On May 23 rd , the FDA approved Telaprevir (Tradename: Incivek ; Research Code: VX-950, NDA 201917), a Hepatitis C virus NS3 protease  (HCV NS3) inhibitor, for the treatment of chronic hepatitis C virus genotype 1  infection, in combination with peginterferon alfa and ribavirin . HCV is a prolonged infection that affects the liver and is caused by a small positive single-stranded RNA virus , which is transmitted by blood-to-blood contact. Chronic hepatitis C is normally asymptomatic, but may lead to liver fibrosis, and if untreated, potentially fatal liver failure. There is currently no vaccine for this type of hepatitis. Telaprevir is an inhibitor of the hepatitis C virus (HCV) non-structural protein 3 (NS3) protease (ChEMBLID: CHEMBL4893 ; Uniprot ID: A3EZI9 ), a viral protein required for the proteolytic cleavage of the HCV encoded polyprotein (UniProt: P27958 ) into mature forms of the NS4A, NS4B, NS5A and NS5B proteins (NS3 is Unip...

ATC code (partial): J05AG On May 20 th , the FDA approved Rilpivirine (Tradename: Edurant ; Research Code: TMC-278, NDA 202022), an HIV-1 Non-nucleoside reverse transcriptase inhibitor ( NNRTI ), for the treatment of HIV infection in treatment naive patients in combination with other HIV therapies. HIV infection is a serious, and if untreated fatal infection caused by a lentivirus , however due to intensive research, leading to a wide variety of antiviral agents the disease is treatable with a substantial increase in quality of life anticipatable. Rilpivirine is an inhibitor of the essential reverse transcriptase  (RT) enzyme of HIV-1. (ChEMBLID: CHEMBL247 ; Uniprot ID: Q72547 ), a viral protein required for the transcription of the single-stranded RNA genome of HIV-1 into double-stranded DNA - this is the opposite of the classical transcription of DNA into RNA. The RT enzyme is translated as part of a long complex gag-pol polyprotein, and requires specific pr...

Here is a job advert, not for a ChEMBL position, but as part of the (fabulous) IUPHAR-DB project. Senior data curator to assist with the development of the IUPHAR Database ( http://www.iuphar-db.org ) and the British Pharmacological Society Guide to Receptors and Channels ( http://www.brjpharmacol.org/view/0/GRAC.html ). You should hold a PhD or equivalent in Pharmacology, Medicinal Chemistry or a related discipline together with relevant experience in bioinformatics or chemoinformatics. Based in the Queen's Medical Research Institute, you will work independently on a day-to-day basis but in close contact with Professor Tony Harmar, with the database developer and in liaison with IUPHAR and BPS. Closing date is 22nd June. For further information and to apply, click here (see http://bit.ly/kDl7mu ) This post is fixed term until 31st July 2012 with possibility of extension should further funding be obtained.

A simple cross post from the /chemical/structure Blog - the guys have done a great job of setting up a python queryable version of the ChEMBL data. Here's the link !

The Society of Medicines Research (SMR) have a great conference on Transporters in Drug Discovery , being held on Thursday 23rd June 2011, at the Millennium Gloucester Hotel, Kensington, London. Further details are on the SMR website . I (jpo) will actually manage to attend this one, so if anyone wants to meet up, that would be great.

A paper has recently been published, which may be of interest; it covers the use of chemogenomics class data in activities such as target prediction, receptor deorphanisation and so forth. A link the the paper is here . %T Chemogenomics Approaches for Receptor Deorphanization and Extensions of the Chemogenomics Concept to Phenotypic Space %J Curr. Topics Med. Chem. %V 11 %A E. van der Horst %A J.E. Peironcely %A G.J.P. van Westen %A O.O. van den Hoven %A W.R.J.D. Galloway %A D.R. Spring %A J.K. Wegner %A H.W.T. van Vlijmen %A A.P. IJzerman %A John P. Overington %A A. Bender %D 2011