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
  • Chemoinformatics Practical

    1. 1. AIB Chemical Similarity Search 28 November 2013 Dr. Puneet Kacker
    2. 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. 3. Drug Discovery Pipeline AIB A Typical Drug Discovery Workflow 3
    4. 4. Where are we? A Typical Drug Discovery Workflow AIB
    5. 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. 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. 7. Chemical Search Methods Substructure search Similarity Docking QSAR Three things should be kept in Mind: 1. Question 2. Model 3. Requirements AIB
    8. 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. 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. 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. 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. 12. Where to Search? AIB Databases PubChem ZINC Collaborative Collection BindingDB 12
    13. 13. Databases: NCBI PubChem AIB 13
    14. 14. PubChem Results AIB Search for Similar Compounds Scores >=95% 14
    15. 15. ZINC Database AIB 15
    16. 16. AIB PubChem Chemical Similarity Search Tool 16
    17. 17. Keyword Based Search AIB 17
    18. 18. Identity/Similarity: Structure Draw AIB 18
    19. 19. Identity/Similarity: CID/SMILES/InChI AIB 19
    20. 20. Identity/Similarity: Structure File AIB 20
    21. 21. Substructure Based Search: Structure Draw AIB 21
    22. 22. Substructure Based Search: SMILES/CID/InChI AIB 22
    23. 23. Substructure Based Search: Structure File AIB 23
    24. 24. Molecular Formula Based Search AIB 24
    25. 25. 3D Conformer AIB 25
    26. 26. PubChem: Limit AIB 26
    27. 27. Chemical Sketching AIB 27
    28. 28. Books AIB
    29. 29. Food for Thought AIB 29
    30. 30. Smart Apps for Your Smartphone iMolview By Molsoft ChemDoodle Mobile By iChemLabs, LLC. ChemDraw By PerkinElmer AIB
    31. 31. Exercise-I AIB Warfarin Anticoagulant, Vitamin K Epoxide Reductase Inhibitor Draw the structure of Warfarin using eMolecules 31
    32. 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. 33. AIB Questions? -:Contact:Room Number LG-16, J3 Block Amity Institute of Biotechnology Amity University Uttar Pradesh Noida-201313
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