ORVIL Manual

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ORganic VIrtual Library (ORVIL) –A COMBINATORIAL LIBRARY CONSTRUCTION BASED ON ORGANIC CONSTITUENTS AND WITHOUT SCAFFOLD HOPPING

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ORVIL Manual

  1. 1. ORganic VIrtual LibraryA program to create Virtual Compound Library using Organic Substituents HYHORSHG E 63UDVDQWK .XPDU %LRLQIRUPDWLFLDQ
  2. 2. What it is all about ? Generation of large number of compounds = Library Focused on Organic Substituents (200 in no.) Only most frequent organic substituents Non- 2 Types: Non- Aromatic Aromatic H3C Cl CH 3 R R
  3. 3. Basement System):SMILES (Simplified Molecular Input Line Entry System): is a line notation (atypographical method using printable characters) for entering andrepresenting molecules and reactions.Why SMILES is chosen ? Easy to storage and retrieval Requires minimum storage space in hard disks Reproducibility String manipulation can be done which can be easily reflected in 3D
  4. 4. Focus Scope No Diverse Compounds = Molecular Diversity Minimum Maintain Scaffold Play with Side Chains / Terminals Creating Analogues Requires priori knowledge of substitution in SMILE Library Generation based on Well Furnished Substitution Site; Not on Scaffold Deals with Organic Subset : B,C,N,O,P,S
  5. 5. Advantages Freely available Command line interpreter Interface Execution across all platforms Customizable PERL program for own library creation Output files in .smi format (SMILES), easily recognized by molecular editors Generate a Library of 1200 unique molecules Fragment- Useful for HTS and Fragment-based approach
  6. 6. Limitations No GUI No atoms other than Organic Subset (e.g. Silicon) since their occurrence is known to be very less Users who want to customize must know the structure’s SMILE (It can be easily tackled by Molecular Editors)Minimum Requirements http://www.ActiveState.com/ActivePerl/)Active Perl 5.10 (Freeware http://www.ActiveState.com/ActivePerl/)Hardware Space Required:Generates 60.8 KB of 1200 library files (if your files are compressed byGeneric Windows Compression)
  7. 7. Algorithm Structure Input as SMILE Substitute with 200 Organic Substituents Functional Group in 200 Organic Substituents marked by the letter ‘X’ Substitute Functional Group with Organic Subset (B,C,N,O,P,S) Generate a Virtual Library comprising 1200 molecules © Prasanth Kumar, (2010), ORVIL : ORganic Virtual Library
  8. 8. Region of SubstitutionS H3CCA CN(Cl)CCOc1ccc(cc1)/C(c2ccccc2)=C(/CC)c3ccccc3F Tamoxifen’s SMILESFO Input Format OL CN(Cl)CCOc1ccc(cc1)/C(c2ccccc2)=C(region)c3ccccc3D H3C N CH3 Use the word REGION or region Tamoxifen (Breast Cancer Drug) in order to recognize the place of organic substituents substitution
  9. 9. Let us generate an Organic Virtual Library of Tamoxifen Command line interpreter Interface of ORVIL
  10. 10. .txt .pl .smi .txt CN(Cl)CCOc1ccc(cc1)/C(c2ccccc2)=C(region)c3ccccc3
  11. 11. Non-= (6 atoms * 137 Non- Aromatic Org. Subs. = 822 files)+ 4 program files
  12. 12. Applications Cl Cl O Cl H3C N N O CH3 CH 3 Fareston C-Compound #3
  13. 13. ReferencesUwe Eichlera, Peter Ertla, Alberto Gobbia and Bernd Rohdeb, 1999.Definition of an Optimal Subset of Organic Substituents. Interactive VisualComparison of Various Selection Algorithms. Internet Journal of Chemistry,2(14).Perl Programming by James TindallMarvin Family, Markush Enumerations, ChemAxon LtdChemSketch, ACDLabs(Entire List will be available in Manuscript)
  14. 14. Thank You !!!

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