• EBI Open Day - 1st March 2012



    The EMBL-EBI is holding one of its regular Open Days on March 1st 2012 - details are at www.ebi.ac.uk/training/openday. These are always really fun events, and give a great insight into life, careers, and activities at our work. The deadline for registration is February 1st 2012.

  • USAN Watch - January 2012

    The USANs for January 2012 have just been published.

    USAN Research Code StructureDrug ClassTherapeutic classTarget
    arhalofenateMBX-102, JNJ-39,659,100synthetic small moleculetherapeuticPPAR-gamma
    bitopertinRo-4917838synthetic small moleculetherapeuticGlyT1
    naldemedineS-297,995natural product-derived small moleculetherapeuticperipheral opioid receptors
    pateclizumabRG-7416, PRO-283698, MLTA-3698Amabtherapeuticlymphotoxin alpha
    pictilisibGDC-0941, RG-7321synthetic small moleculetherapeuticPI3K, mTor
    tivozanib, tivozanib hydrochlorideAV-951, Kil-8951synthetic small moleculetherapeuticVEGFR
    Update: Fixed research code for Pactelizumab - thanks to Robert Jones (details in the comments).

  • Paper: Global Analysis of Small Molecule Binding to Related Protein Targets


    Many drugs are small molecules that specifically bind to proteins involved in disease related processes. In this way, drugs modulate the function of a targeted protein and ultimately the process causing the disease. The development of drugs crucially relies on assays that measure the potency of the effect a small molecule exerts on its protein target. We compared the potencies of small molecules measured for human proteins and the corresponding (orthologous) protein in rat. Our results suggest that, after subtraction of statistical noise, most human proteins show equivalent potency for small molecule binding as their orthologs in rats. However, we identified a small number of exceptions to this rule, for example the histamine H3 receptor, a protein of the central nervous system. We also compared the potency of small molecules measured against a human protein and another member of the same protein family. In drug development it is often desired to target a protein selectively over other related proteins. The observed differences were generally greater than the statistical noise, indicating that most of the small molecules in our study have some degree of selectivity within protein families.

    Link to the paper is here. 
    

    %A F.A. Krueger
%A J.P. Overington
%T Global Analysis of Small Molecule Binding to Related Protein Targets
%D 2012
%V 8
%P e1002333
%J PLoS Comput. Biol.
%O doi:10.1371/journal.pcbi.1002333

    
	  
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    Anyone know anything about Non-Proprietary Drug naming in China?
    
	  	
	  	
    

    

    
There are a comparatively large number of Chinese company invented drug entering clinical trials now - these are typically assigned USAN/INN looky-likey names, and seem to obey stem naming conventions. Does anyone know how these are assigned, is there an equivalent of USAN in China, where does the data get published, etc.?
    

    
As specific examples of these, there are a set of kinase inhibitors - Epitinib (EGFR), Flumatinib (ABL1), Fruquintinib (VEGFR), Icotinib (EGFR), Sulfatinib (VEGFR FGFR), Volitnib (MET).
    

    
I've also asked this question on Quora - I'll post any replies there in the comments section here.
    

    
Update: To be clear, I have no interest in the commercial import/export of drug substances into or out of China, I'm only interested in the name assignment process.
    
	  
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    Talk - Alex Tropsha - Many Challenges and Some Solutions for Modeling Chemical Genomics Data: navigating structure – in vitro – in vivo response data space
    
	  	
	  	
    

    

    
Welcome back after the holiday break!
    

    
We have a small informal seminar on campus, on Tuesday 17th January 2011 from Alex Tropsha from UNC, the talk will be titled “Many Challenges and Some Solutions for Modeling Chemical Genomics Data: navigating structure – in vitro – in vivo response data space".
    

    
If you are interested in attending from off campus - I will need to register you with security - so mail me.
    

    
Update: The seminar will be at 2pm in seminar room C202 (shared facilities). (Mail to arrange access for off campus attendees though!
    


    
Update 2: Please note - we cannot provide online access to the talk. Sorry.
    
	  
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    Omics and Personalised Healthcare - February 2012
    
	  	
	  	
    

    

    
We're speaking at the forthcoming EMBL Conference on Omics and Personalised Healthcare in Heidelberg, held 16th to 18th February 2012. We'll present some of our recent work on pharmacogenetic variation, and some strategies on both data-mining and some of the implications for drug discovery.
    
	  
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    Three ChEMBL talks at the March ACS in San Diego
    
	  	
	  	
    

    

    

    
A number of the ChEMBL team will be at the ACS in San Diego next March - we'll be giving a couple of talks -  one is one drug safety (jpo) one is on peptide SAR analysis and design (Patricia Bento) and the final one is on UniChem (Jon Chambers). So hopefully see you there!
    

    
We'll be spending some time in the lab of one of our close collaborators - Mike Gilson at UCSD, but we're happy to meet up with others, give talks, training, etc. as time and travel schedules permit. So if you're interested in this, get in touch.
    

    
Update: Fixed post, to reflect three accepted talks.
    

    

    


    PAPER ID: 20839
PAPER TITLE: "Drug combinations to reduce adverse drug reactions and improve intrapatient differences in response"
DIVISION: CINF: Division of Chemical Information
SESSION: Systems Chemical Biology and Other 

PAPER ID: 22715
PAPER TITLE: "UniChem: A prototype unified chemical structure cross-referencing and identifier tracking system"
DIVISION: CINF: Division of Chemical Information
SESSION: InChI Symposium

PAPER ID: 15760
PAPER TITLE: "Comprehensive analysis of explored and available physicochemical space for alpha-amino acids"
DIVISION: ORGN: Division of Organic Chemistry
SESSION: Peptides, Proteins, and Amino Acids

    
	  
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    Kinase SARfari ver.5.0 Released
    
	  	
	  	
    We would like to announce the release of new version Kinase SARfari. The latest version has been updated using the chembl_12 data, which contains:
    

    

      

    • Bioactivity datapoints: 
503041 (+15%)
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    • Compounds: 
54189 (+6%) 
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 Various dumps of the data from Kinase and GPCR SARfari are also downloadable from the download page.
    

    
 Of course, we welcome feedback from our users!
    
	  
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