ChEMBL Resources

The SARfaris: GPCR, Kinase, ADME

Monday, 17 December 2012

Pipeline Pilot Cambridgeshire UGM

We will be organising the 2nd Cambridgeshire Pipeline Pilot Users Group meeting on Thursday 17th January 2013, at 3pm here at the ChEMBL HQs. This is provided that the Mayans were actually wrong. 

This is a preliminary agenda for the meeting:

1. Welcome and Host talk:  George Papadatos + Gerard van Westen:
      Cool things with Pipeline Pilot and ChEMBL
2. Peter Woollard (GSK):
      Using Pipeline Pilot for computational biology capabilities, where it has helps the most and where it is less used
3. Richard Carter (ONT):
       Pipeline Pilot on a memory stick
4. Mike Cherry (Accelrys):
        Repetitive Data Flow
5. Question and Answer session, including:
   - how people have found Next Generation Sequencing components  and the Text Analytics components
   - using Pipeline Pilot for running command line software on remote linux servers and retrieving results
6. Adrian Stevens (Accelrys)
      Upcoming chemistry components in PP9.0

If you fancy attending, drop me a line.


Friday, 14 December 2012

Paper: Mapping small molecule binding data to structural domains

Our interacting domains paper is out in pdf form. Here's the link.

%T Mapping small molecule binding data to structural domains
%A F.A. Kruger
%A R. Rostom
%A J.P. Overington
%J BMC Bioinformatics 
%D 2012
%V 13(Suppl 17)
%P S11 
%O doi:10.1186/1471-2105-13-S17-S11

Wednesday, 12 December 2012

Paper: Automated design of ligands to polypharmacological profiles

Another great paper in Nature this week, making extensive use of ChEMBL. It's by our long-term collaborators up at Dundee - Jeremy, Richard and Andrew - well done, great stuff! Basically it combines a knowledge-base of SAR data (ChEMBL), some predictive models for affinity/properties, and extracts a set of reasonable transforms (chemical conversions) from the same knowledge-base. I'll ask Jeremy/Andrew to do a guest post on the ChEMBL-og on the paper - they're probably pretty busy with press-releases, etc. ;)

Here's a link to the paper.

Have a read, it will keep you busy for a few hours.

%A J. Besnard
%A G.F. Ruda
%A V. Setola
%A K. Abecassis
%A R.M. Rodriguez
%A X.-P. Huang
%A S. Norval
%A M.F. Sassano
%A A.I. Shin
%A L.A. Webster
%A F.R.C. Simeons
%A L. Stojanovski
%A A. Prat
%A N.G. Seidah
%A D.B. Constam
%A G.R. Bickerton
%A K.D. Read
%A W.C Wetsel
%A I.H. Gilbert
%A B.L. Roth
%A A.L. Hopkins
%T Automated design of ligands to polypharmacological profiles
%J Nature
%D 2012
%V 492
%P 215-220

What will you do today with ChEMBL?

Tuesday, 11 December 2012

New Drug Approvals 2012 - Pt. XXVII - Choline C-11

On September 12, FDA approved Choline C-11, an intravenous radioactive diagnostic agent to be used as tracer during Positron Emission Tomography (PET) scan to help detect sites of recurrent Prostate Cancer (OMIM : 176807 ; MeSH : D011471) .

Prostate cancer is the most common cause of death from cancer in men over age 75, and is rarely found in men younger that 40. Unlike many other cancers, prostate cancer usually progresses very slowly. Sometimes the cancer cells may metastasize from the prostate to other parts of body. Overall, it is estimated to be the sixth leading cause of cancer-related death in men.

Choline is a naturally occurring component of the numerous Vitamin-B complex, and is necessary for normal cell structure and signalling. Choline C-11 is a radiolabeled synthetic analog of choline that releases a positron by beta decay which can be visualised by PET. Choline is rapidly taken up by the prostate cells and this allows the prostate to be imaged. 

Choline, a precursor molecule essential for the biosynthesis of phospholipids which are the structural components of cell membranes, as well as modulation of trans-membrane signalling. Increased activity of phospholipid synthesis has been associated with increased cell proliferation and the transformation process that occurs in tumour cells.
Choline C-11 is a positron emitting radiopharmaceutical that is used for diagnostic purpose in conjunction with PET imaging. The active ingredient is Choline C-11 and each millilitre of the injection contains 148 MBq to 1225 MBq of the active ingredient.

IUPAC Name (Choline) : 2-hydroxy-N,N,N-trimethylethanaminium
Canonical Smiles : [Cl-].[11CH3][N+](C)(C)CCO
Standard InChI : 1S/C5H14NO.ClH/c1-6(2,3)4-5-7;/h7H,4-5H2,1-3H3;1H/q+1;/p-1/i1-1;

Following intravenous administration, Choline C-11 distributes mainly to the pancreas, kidney, liver, spleen and colon. The radioactivity accumulated rapidly within the prostate and peak uptake appeared with in 5 mins following the administration. Choline C-11 undergoes metabolism resulting in the detection of 11C-betaine as the major metabolite in blood. The rate of excretion of Choline C-11 in urine was 0.014 mL/min.

Choline C-11 has been developed and marketed by Mayo Clinic.

Full prescribing information is found here.

Browsers and Bugs

We had a support email recently that some things on the interface didn't work with chrome (an export function) - we couldn't repeat the issue with the equipment we have here at ChEMBL Towers. But there are a lot of OS's and a lot of browsers out there, and we can't recreate every possible environment - interestingly, chrome is really popular amongst you people (the image above is a google analytics report of a weeks access of this very blog). I'm a safari man myself....

So as a reminder, we love hearing about bugs and issues, we really do, so send them to!