Open Notebook Science and Preliminary Falcipain-2 Results


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This talk was presented by Jean-Claude Bradley at the American Chemical Society meeting in Philadelphia on August 20, 2008. An introduction to Open Notebook Science is presented followed by an illustration of how ONS can be used in drug discovery. New data relating to the anti-malarial activity of Ugi products on 2 falcipain-2 docking sites is detailed. The docking calculations were provided by Rajarshi Guha and the enzyme and in vitro assays on Plasmodium falciparum were provided by Phil Rosenthal and Jiri Gut. Most of the syntheses were carried out by Khalid Mirza in the Bradley group.

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Open Notebook Science and Preliminary Falcipain-2 Results

  1. 1. Processing drug discovery raw data collaboratively and openly using Open Notebook Science Jean-Claude Bradley E-Learning Coordinator College of Arts and Sciences Associate Professor of Chemistry Drexel University August 20, 2008 American Chemical Society
  2. 2. Open and Closed Science Traditional Lab Notebook (unpublished) Traditional Journal Article Open Access Journal Article Open Notebook Science (full transparency) CLOSED OPEN Traditional Paper Textbook F2F lectures Lectures Notes public Assigned problems public Archived Lectures Public and free online textbooks RESEARCH TEACHING
  3. 3. Open Primary Research in Drug Design using Web2.0 tools (blogs, wikis, Second Life, mailing lists) Docking Synthesis Testing Rajarshi Guha Indiana U JC Bradley Drexel U Phil Rosenthal UCSF (malaria) Dan Zaharevitz NCI (tumors) Tsu-Soo Tan Nanyang Inst.
  4. 4. BLOG WIKI Mailing List GoogleDocs UsefulChem ChemSpider CDD
  5. 5. Where’s the Beef?
  6. 6. Link to Lab Notebook Page in Wiki
  7. 7. Link to Molecules
  8. 8. Link to Docking Procedure (Rajarshi Guha)
  9. 9. Link to Docking Results: Lists of SMILES in GoogleDocs (Rajarshi Guha)
  10. 10. Procedure Section
  11. 11. Link to Raw Data with JSpecView (data in JCAMP-DX format) (by Robert Lancashire)
  12. 12. Using ChemSpider to archive compound characterization
  13. 13. ChemSpider predicted vs. experimental NMRs
  14. 14. The Most Important Section! The Log
  15. 15. Conclusion is Fully Supported
  16. 16. Table of Contents
  17. 17. Indexing the Experiments in Google
  18. 18. Searching with Google Custom Search
  19. 19. How are people finding our experiments? NMR in TFA Phenylacetaldehyde c4h6o2 nmr methylene chloride/methanol h'nmr of benzophenone sulfuric acid pka tertbutylamine tosyl isocyanide amino furan dichloromethane polar? Reaction between Benzaldehyde and NaBH4 phosphoric acid pka veratraldehyde wiki kinetics boc deprotection Rf value in polar solvent why glycerol is immiscible with ether side reaction of imines 5.8 ppm nmr nmr cdcl3 chloroform side reaction diasterotopic wiki adding anhydrous MgSO4 to the dichlormethane ether extraction hnmr doublet of doublet Boc-protected NMR chromatotron recipe triplet cdcl3 "13c nmr" Specific Compounds Experimental Conditions
  20. 20. How are people finding UsefulChem? free downloading chemistry video organic chemistry project + high school how to make poster in second life organic chem. quiz 3d periodic tables animation protein docking docking animation why are acid-base reactions exothermic? lysosomal targets protease and malaria cheminformatics project proposal automated reactions malaria review project synthesis CHEMISTRY WEB 2.0 projects on QSAR & drug design chemistry experiment results database Educational Big Picture
  21. 21. How Should Open Notebook Science be Used?
  22. 28. How did this experiment evolve? Third party timestamp
  23. 29.
  24. 34.
  25. 35. Comparing Experiments Ugi Master Table
  26. 36. YouTube for demonstrating experimental set-up
  27. 37. Older Males Prefer Organic Chemistry!
  28. 38. Mailing List Facilitates inter-group collaboration
  29. 39. Outcome of Guha-Bradley-Rosenthal collboration
  30. 40. Collaborative Drug Discovery (CDD) Database
  31. 42. Interacting with NMR spectra (JCAMP-DX) in Second Life
  32. 43. Talk to the spectrum: zoom 2.1-2.3 (Andy Lang)
  33. 44. Using ExcelVBA to automate kinetics analysis
  34. 45. Reaction profile plotted automatically
  35. 46. 3D molecules in Second Life
  36. 47. Imine Formation Mechanism: talk to the molecules!
  37. 48. Gus Rosania’s Notebook
  38. 49. Cameron Neylon’s Notebook
  39. 50. Results in Machine-Friendly Format
  40. 51. Mettler-Toledo MiniMapper
  41. 52. Mettler-Toledo MiniBlock System
  42. 53. GoogleDoc to program and report
  43. 54. XML reports from MiniMapper robot
  44. 55. Methanol 0.4M xs of imine best
  45. 56. Where is Science headed? WE ARE HERE
  46. 57. Conclusion <ul><li>Communicate first </li></ul><ul><li>Standardize second </li></ul><ul><li>In a Science2.0 world redundancy is king </li></ul>