1. 1 © Patrick An Introduction to Medicinal Chemistry 3/e Chapter 14 COMBINATORIAL CHEMISTRY Part 2: Sections 14.5 – 14.6

2. 1 © Contents 5.Identification of structures from mixed combinatorial synthesis 5.1.Recursive Deconvolution (5 slides) 5.2.Tagging (3 slides) 6.Identification of structures from a combinatorial synthesis 6.1.Encoded Sheets (4 slides) 6.2.Photolithography (3 slides) [16 slides]

3. 1 © 5.1 Recursive Deconvolution Method of identifying the active component in a mixtureMethod of identifying the active component in a mixture Quicker than separately synthesising all possible componentsQuicker than separately synthesising all possible components Need to retain samples before each mix and split stageNeed to retain samples before each mix and split stageExample Consider all 27 tripeptides synthesised by the mix and split strategy from glycine, alanine and valine 5. Identification of structures from mixed combinatorial synthesis

4. 1 © Gly AlaVal Mix and Split All possible dipeptides in three vessels Retain a sample from each vessel

5. 1 © Gly AlaVal Mix and Split All possible tripeptides in three vessels

6. 1 © 5. Identification of structures from mixed combinatorial synthesis Mixture Inactive Mixture Inactive Mixture Active 9 Possible tripeptides in active mixture9 Possible tripeptides in active mixture All end in valineAll end in valine Add valine to the three retained dipeptide mixturesAdd valine to the three retained dipeptide mixtures 5.1 Recursive Deconvolution

7. 1 © Active component narrowed down to one of three possible tripeptidesActive component narrowed down to one of three possible tripeptides Synthesise each tripeptide and testSynthesise each tripeptide and test 5. Identification of structures from mixed combinatorial synthesis 5.1 Recursive Deconvolution

8. 1 © 5.2 Tagging 5. Identification of structures from mixed combinatorial synthesis Method of identifying the structure present on a beadMethod of identifying the structure present on a bead Tagging molecule constructed on same bead as target moleculeTagging molecule constructed on same bead as target molecule Use amino acids or nucleotides to construct tagging moleculeUse amino acids or nucleotides to construct tagging molecule Each amino acid or nucleotide is used to indicate a specific reagent or reactant used at each stepEach amino acid or nucleotide is used to indicate a specific reagent or reactant used at each step An amino acid or nucleotide is added after each step in the reaction sequenceAn amino acid or nucleotide is added after each step in the reaction sequence Peptide tag identified using automatated peptide sequencingPeptide tag identified using automatated peptide sequencing Oligonucleotide sequence identified using DNA sequencingOligonucleotide sequence identified using DNA sequencing Require a linker with two functional groups (e.g. SCAL)Require a linker with two functional groups (e.g. SCAL)

9. 1 © Lysine Tryptophan 5.2 Tagging SCAL = Safety CAtch Linker 5. Identification of structures from mixed combinatorial synthesis

10. 1 © 5.2 Tagging Example

11. 1 © 6. Identification of structures from a combinatorial synthesis 6.1 Encoded Sheets Resin beads sandwiched between two polypropylene sheetsResin beads sandwiched between two polypropylene sheets Sheets encoded as squaresSheets encoded as squares Linking first amino acid

12. 1 © Linking second amino acid

13. 1 © Cut and separate

14. 1 © Linking third amino acid

15. 1 © 6. Identification of structures from combinatorial synthesis 6.2 Photolithography Suitable for miniaturisation and spatial resolutionSuitable for miniaturisation and spatial resolution Use plates with solid phase attachedUse plates with solid phase attached Use protecting groups susceptible to lightUse protecting groups susceptible to light (e.g. nitroveratryloxycarbonyl for amino groups)(e.g. nitroveratryloxycarbonyl for amino groups) Use masks to deprotect specific areas of plateUse masks to deprotect specific areas of plate Record kept of areas thus activated for next reactionRecord kept of areas thus activated for next reaction Final products left attached to plate after synthesis completeFinal products left attached to plate after synthesis complete Incubate plate with fluorescently labelled receptorIncubate plate with fluorescently labelled receptor Active compounds bind to the receptorActive compounds bind to the receptor Active areas identified by fluorescenceActive areas identified by fluorescence 20 Micron resolution possible (250,000 separate compounds per square centimetre)20 Micron resolution possible (250,000 separate compounds per square centimetre)

16. 1 © NHXNHXNHXNHXNHX NHXNHXNHXNHXNHXNHX NHXNHXNHXNHXNHXNHX 6. Identification of structures from combinatorial synthesis 6.2 Photolithography - example LIGHT NHXNHXNHXNHX NHXNHXNHXNHXNHXNHX NHX CO 2 H coupling NHX NHX NHX NHXNHX NHX NHX NHXNHXNH 2 NH 2 NH 2 NHXNHXNHXNH 2 NH 2 NHX NHXNHXNHXNHXNHXNHX Deprotection

17. 1 © YY Y 6. Identification of structures from combinatorial synthesis 6.2 Photolithography - example Y amino acids OMe OMe O O 2 N O X= Nitroveratryloxycarbonyl fluorescent tag Target receptor Y