AIB

Chemical Similarity Search

28 November 2013

Dr. Puneet Kacker
www.puneetsclassroom.in
Chemoinformatics

AIB

 Chemoinformatics is an interface science aimed
primarily at discovering new chemical entries that...
Drug Discovery Pipeline

AIB

A Typical Drug Discovery Workflow

3
Where are we?

A Typical Drug Discovery Workflow

AIB
Hit Identification: What is Expected

Some Magic
Database of
Chemical
Compounds
(Millions of Cmpds)

??

AIB

Few Compound...
Chemical Similarity

AIB

Similarity

Common
Substructure

Overall Similarity

Ligand-based
Methods

Similar Predicted
Act...
Chemical Search Methods

Substructure search
Similarity
Docking
QSAR
Three things should be kept in Mind:
1. Question
...
Substructure Search

AIB

Question: Which molecules in a database
contain the specified substructure?
Model: Compounds t...
Similarity Based Search

AIB

Question: Which molecules in a database
are ‘similar’ to the query molecule(s)?
Model: Com...
Docking Based Search

AIB

Question: Which molecules in a database
can fit into the binding site of a known
enzyme or rec...
QSAR Based Method

AIB

Question: Which molecules have the
highest predicted activity?
Model: Compounds with high predic...
Where to Search?

AIB

Databases

PubChem

ZINC

Collaborative
Collection

BindingDB

12
Databases: NCBI PubChem

pubchem.ncbi.nlm.nih.gov/

AIB

13
PubChem Results

AIB

Search for
Similar Compounds Scores >=95%

14
ZINC Database

http://zinc.docking.org/

AIB

15
AIB

PubChem Chemical Similarity Search Tool

16
Keyword Based Search

AIB

17
Identity/Similarity: Structure Draw

AIB

18
Identity/Similarity: CID/SMILES/InChI

AIB

19
Identity/Similarity: Structure File

AIB

20
Substructure Based Search: Structure Draw
AIB

21
Substructure Based Search:
SMILES/CID/InChI

AIB

22
Substructure Based Search: Structure File
AIB

23
Molecular Formula Based Search

AIB

24
3D Conformer

AIB

25
PubChem: Limit

AIB

26
Chemical Sketching

AIB

27
Books

AIB
Food for Thought

AIB

29
Smart Apps for Your Smartphone

iMolview
By Molsoft

ChemDoodle Mobile
By iChemLabs, LLC.

ChemDraw
By PerkinElmer

AIB
Exercise-I

AIB

Warfarin
Anticoagulant, Vitamin K Epoxide Reductase Inhibitor

Draw the structure of Warfarin using eMole...
Exercise-II

AIB

Warfarin

Find out similar structures of Warfarin using PubChem Chemical Similarity Search
Also try to D...
AIB

Questions?
-:Contact:Room Number LG-16, J3 Block
Amity Institute of Biotechnology
Amity University Uttar Pradesh
Noid...
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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 www.puneetsclassroom.in
    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 pubchem.ncbi.nlm.nih.gov/ AIB 13
    14. 14. PubChem Results AIB Search for Similar Compounds Scores >=95% 14
    15. 15. ZINC Database http://zinc.docking.org/ 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 pkacker@amity.edu www.puneetsclassroom.in
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