Chemoinformatics Practical
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  • Snapshot for the types of library available on zinc database. And also total number of compounds available in each of the database

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  • 1. AIB Chemical Similarity Search 28 November 2013 Dr. Puneet Kacker www.puneetsclassroom.in
  • 2. Chemoinformatics AIB  Chemoinformatics is an interface science aimed primarily at discovering new chemical entries that will ultimately result in the development of novel treatments for unmet medical needs. 2
  • 3. Drug Discovery Pipeline AIB A Typical Drug Discovery Workflow 3
  • 4. Where are we? A Typical Drug Discovery Workflow AIB
  • 5. Hit Identification: What is Expected Some Magic Database of Chemical Compounds (Millions of Cmpds) ?? AIB Few Compounds Ready for Synthesis/Testing Magic of Chemical Similarity 5
  • 6. Chemical Similarity AIB Similarity Common Substructure Overall Similarity Ligand-based Methods Similar Predicted Activity Similar Fitting into Binding Pocket Structure-based Method 6
  • 7. Chemical Search Methods Substructure search Similarity Docking QSAR Three things should be kept in Mind: 1. Question 2. Model 3. Requirements AIB
  • 8. Substructure Search AIB Question: Which molecules in a database contain the specified substructure? Model: Compounds that contain this substructure are likely to be active. Query requires: 2D or 3D substructure common to actives (‘pharmacophore’ in 3D). 8
  • 9. Similarity Based Search AIB Question: Which molecules in a database are ‘similar’ to the query molecule(s)? Model: Compounds globally similar in structure to the query are likely to have a similar activity. Query requires: One or more active molecules. 9
  • 10. Docking Based Search AIB Question: Which molecules in a database can fit into the binding site of a known enzyme or receptor? Model: Compounds that have a high interaction score are likely to bind to the enzyme. Query requires: Atomic-level structure of receptor (or model built from homolog). 10
  • 11. QSAR Based Method AIB Question: Which molecules have the highest predicted activity? Model: Compounds with high predicted activity are likely to be active. Query requires: Activity data on enough compounds to form QSAR. 11
  • 12. Where to Search? AIB Databases PubChem ZINC Collaborative Collection BindingDB 12
  • 13. Databases: NCBI PubChem pubchem.ncbi.nlm.nih.gov/ AIB 13
  • 14. PubChem Results AIB Search for Similar Compounds Scores >=95% 14
  • 15. ZINC Database http://zinc.docking.org/ AIB 15
  • 16. AIB PubChem Chemical Similarity Search Tool 16
  • 17. Keyword Based Search AIB 17
  • 18. Identity/Similarity: Structure Draw AIB 18
  • 19. Identity/Similarity: CID/SMILES/InChI AIB 19
  • 20. Identity/Similarity: Structure File AIB 20
  • 21. Substructure Based Search: Structure Draw AIB 21
  • 22. Substructure Based Search: SMILES/CID/InChI AIB 22
  • 23. Substructure Based Search: Structure File AIB 23
  • 24. Molecular Formula Based Search AIB 24
  • 25. 3D Conformer AIB 25
  • 26. PubChem: Limit AIB 26
  • 27. Chemical Sketching AIB 27
  • 28. Books AIB
  • 29. Food for Thought AIB 29
  • 30. Smart Apps for Your Smartphone iMolview By Molsoft ChemDoodle Mobile By iChemLabs, LLC. ChemDraw By PerkinElmer AIB
  • 31. Exercise-I AIB Warfarin Anticoagulant, Vitamin K Epoxide Reductase Inhibitor Draw the structure of Warfarin using eMolecules 31
  • 32. Exercise-II AIB Warfarin Find out similar structures of Warfarin using PubChem Chemical Similarity Search Also try to Download Results in SDF Format 32
  • 33. AIB Questions? -:Contact:Room Number LG-16, J3 Block Amity Institute of Biotechnology Amity University Uttar Pradesh Noida-201313 pkacker@amity.edu www.puneetsclassroom.in