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Presented at Drexel University on Oct 10, 2008 in the chemistry department faculty mini-symposium. A quick summary of Open Notebook Science and its application to drug discovery.
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The Synthesis of anti-malarial compounds using
Open Notebook Science
Jean-Claude Bradley
Oct 10, 2008
Drexel MiniSymposium
Associate Professor of ChemistryDrexel University
Motivation: Faster Science, Better Science
Malaria Target: falcipain-2 involved in hemoglobin metabolism
Dana.org
UsefulChem Project:UsefulChem Project: Open Primary Open Primary Research in Drug Design using Web2.0 Research in Drug Design using Web2.0
toolstools
Docking
Synthesis
Testing
Rajarshi GuhaIndiana U
JC BradleyDrexel U
Phil RosenthalUCSF
(malaria)
Dan ZaharevitzNCI
(tumors)
Tsu-Soo TanNanyang Inst.
BLOGWIKI
Mailing List
GoogleDocs
Architecture: Distributed,
Interlinked and Redundant
ChemSpider
CDD
FriendFeedNature Precedin
gs JoVE
Where’s the Beef?Where’s the Beef?
Link to Lab Notebook Page in Link to Lab Notebook Page in WikiWiki
Link to MoleculesLink to Molecules
Link to Docking Procedure Link to Docking Procedure (Rajarshi Guha)(Rajarshi Guha)
Link to Docking Results: Link to Docking Results: Lists of SMILES in GoogleDocs Lists of SMILES in GoogleDocs
(Rajarshi Guha)(Rajarshi Guha)
Link to Raw Data with Link to Raw Data with JSpecViewJSpecView
(data in JCAMP-DX format)(data in JCAMP-DX format)(by Robert Lancashire)(by Robert Lancashire)
Conclusion is Fully SupportedConclusion is Fully Supported
How did this How did this experiment experiment
evolve?evolve?
Third party timestamp
Comparing wiki page Comparing wiki page versionsversions
Comparing ExperimentsComparing ExperimentsUgi Master TableUgi Master Table
•Concentration (0.4, 0.2, 0.07 M)•Solvent (methanol, ethanol, acetonitrile, THF)•Excess of some reagents (1.2 eq.)
Reaction to Optimize
Mettler-Toledo MiniBlock System
Mettler-Toledo MiniMapper
XML reports from MiniMapper robot
GoogleDoc to program and report
Paper written on Wiki
References to papers, blog posts, lab notebook pages, raw
data
Paper on Journal of Visualized Experiments (JoVE)
Pre-print on Nature Precedings
Best Yield: 66%
0.4 M methanol 1.2 eq imine
Methanol 0.4M xs of imine Methanol 0.4M xs of imine bestbest
Outcome of Guha-Bradley-Outcome of Guha-Bradley-Rosenthal collborationRosenthal collboration
Measuring Solubilities in Southampton with Cameron
Neylon
Sept 3, 2008 usefulchem.wikispaces.com/exp207
Investigating solubilities in organic solvents
Boc-glycine vanillin glucose NaCl
The Results in a GoogleDoc
reliable
unreliable
AcknowledgementsAcknowledgements
Khalid Mirza (Drexel)Khalid Mirza (Drexel) Kevin Owens (Drexel)Kevin Owens (Drexel) Tim Bohinsky (Drexel)Tim Bohinsky (Drexel) James Giammarco (Drexel)James Giammarco (Drexel) Tom Osborne (Mettler-Toledo)Tom Osborne (Mettler-Toledo) Antony Williams (ChemSpider)Antony Williams (ChemSpider) Andrew Lang (Oral Roberts U.)Andrew Lang (Oral Roberts U.) Cameron Neylon (Southampton U.)Cameron Neylon (Southampton U.)
