1 / 60

DNA-Templated Synthesis: Principles of Evolution in Organic Chemistry

DNA-Templated Synthesis: Principles of Evolution in Organic Chemistry. EDC, Sulfo-NHS, NaBH 3 CN. One solution. Introduction to DTS Organic Reactions in DTS Fundamental reactions, distance dependence and independence New, synthetically useful architectures

karena
Download Presentation

DNA-Templated Synthesis: Principles of Evolution in Organic Chemistry

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. DNA-Templated Synthesis: Principles of Evolution in Organic Chemistry

  2. EDC, Sulfo-NHS, NaBH3CN

  3. One solution

  4. Introduction to DTS Organic Reactions in DTS Fundamental reactions, distance dependence and independence New, synthetically useful architectures Example of a Small Molecule Synthesis Synthetic strategies, linkers, purification Towards the Multistep Synthesis of Small Molecule Libraries Conclusions

  5. Strategies to Control Reactivity The chemist’s approach to controlling reactivity + Starting materials mM – M concentration One possible product

  6. Strategies to Control Reactivity The chemist’s approach to controlling reactivity + Starting materials mM – M concentration One possible product Nature’s approach to controlling reactivity: Macromolecule-templated synthesis Selective product formation nM - M concentration Many reactants in one solution

  7. Synthetic Strategies The chemist’s approach to active molecule discovery: Starting material Product Data: Keq, ee, IC50, …

  8. Synthetic Strategies The chemist’s approach to active molecule discovery: Starting material Product Data: Keq, ee, IC50, … Nature’s approach to active molecule discovery: DNA RNA Protein Selection, Amplification, Diversification

  9. The Basics of DNA-Templated Synthesis (DTS) Reactant for DTS reactive group oligonucleotide linker General Reaction Scheme SH Annealing SH Coupling S

  10. Selection and Amplification Protein Protein Amplification PCR DNA sequencing or PAGE Identity of the active molecule

  11. Polymerase Chain Reaction (PCR) Denature 94oC, 30 s 5’ 3’ Sample 3’ 5’ Anneal primers 55oC, 60 s Stop 4oC 5’ 3’ Extension 75oC, 30 s 3’ 5’ Taq polymerase

  12. Synthesis of Products Unrelated to the DNA Backbone 1,4-conjugate addition to carbonyls SH S Peptide Coupling 73% DMT-MM Or EDC / sulfo-NHS Heck 54% Na2PdCl4 Gartner, Z. J., Kanan, M. W., Liu, D. R. Angew. Chem. Int. Ed.2002, 41, 1796 Gartner, Z.J., Liu, D.R. J. Am. Chem. Soc.2001, 123, 6961.

  13. Sequence Specificity and Distance Independence Sequence Specificity NH2 SH HS A single base mismatch in the 10-base reagent oligonucleotide slows the reaction down by a factor of 200

  14. Sequence Specificity and Distance Independence Distance Independence • Limited ability for diversification • Complicated substrate identification Coding Region for R1, R2 and R3

  15. Sequence Specificity and Distance Independence Distance Independence • Limited ability for diversification • Complicated substrate identification Coding Region for R1, R2 and R3 • Considerably simplifies the identification of active molecules • Necessary to anneal further along the template Coding Region for R2 Coding Region for R3 Coding Region for R1

  16. Distance Independence HS X-X-X-X-X-X-X-X-X-X-5’ T-G-G-T-A-C-G-A-A-T-T-C-G-A-C-T-C-G-G-G….3’ n bases • As n is varied from 1 to 30, the rate does not significantly change for Heck couplings, peptide couplingsand nucleophilic addition. • Unfortunately, not all reactions turned out to be distance independent.

  17. Distance-Dependent Reactions 1,3-dipolar cycloaddition 53% Reductive amination NH2 81% NaBH3CN Nitro-Michael 42% pH 8.5 buffer Gartner, Z. J., Kanan, M. W., Liu, D. R. Angew. Chem. Int. Ed.2002, 41, 1796

  18. Kinetics of Distance Independance A k1 A k2 A B B k-1 B In distance independent reactions, k2 >> k1 B A As n increases, k2 decreases. As long as k2> k1, reaction rate remains distance independent. n bases

  19. Kinetics of Distance Dependance A k1 A k2 A B B k-1 B If k2 k1 the coupling reaction becomes rate-determining B A Since k2 decreases as n increases, the rate of the reaction becomes dependent on the number of bases between the reagents. n bases

  20. The  Architecture: Overcoming Distance-Dependence A A B B Gartner, Z. J., Grubina, R., Calderone, C. T., Liu, D. R. Angew. Chem. Int. Ed. 2003, 42, 1370.

  21. The  Architecture: Overcoming Distance-Dependence A A B B 10-20 base loop A B 10-base coding region 4-5 constant bases at the reactive end • Coding-region annealing is the main driving force. • The constant region forms a secondary structure once the coding region is annealed. Gartner, Z. J., Grubina, R., Calderone, C. T., Liu, D. R. Angew. Chem. Int. Ed. 2003, 42, 1370.

  22. Small Molecule Synthesis: Retrosynthetic Analysis Wittig peptide coupling oxazolidine formation

  23. Multistep Synthesis of Small Molecules NH2 NH2 DMT-MM DMT-MM Li, X., Gartner, Z.J., Tse, B.N., Liu, D.R., J. Am. Chem. Soc. 2004, 126, 5090.

  24. Multistep Synthesis of Small Molecules NH2 NH2 DMT-MM

  25. Multistep Synthesis of Small Molecules NH2 NH2 DMT-MM B A C X

  26. Strategic Linkers Scarless Linker template template reagent pH 11.8 + >95% NH2 reagent Gartner, Z.J., Kanan, M.W., Liu, D.R. J. Am. Chem. Soc.2002, 124, 10304.

  27. Strategic Linkers Scarless Linker template template reagent pH 11.8 + >95% NH2 reagent Useful Scar Linker template template reagent NaIO4 + >95% reagent Gartner, Z.J., Kanan, M.W., Liu, D.R. J. Am. Chem. Soc.2002, 124, 10304.

  28. Strategic Linkers Autocleaving Linker template template reagent + >95% reagent Gartner, Z.J., Kanan, M.W., Liu, D.R. J. Am. Chem. Soc.2002, 124, 10304.

  29. Wittig Olefination template reagent reagent template template template reagent + reagent

  30. Multistep Synthesis of Small Molecules 1) NH2 2 3 1 DMT-MM DMT-MM NH2 2) Cleavage buffer pH = 11.8 ? Purification

  31. Multistep Synthesis of Small Molecules 1) NH2 2 3 1 DMT-MM 2) Cleavage buffer pH = 11.8 Product Purification Avidin Avidin biotin R biotin

  32. Purification of DNA-Templated Reactions Purification with scarless or useful scar linker A B A A B B A B B A B Bead-bound avidin Biotin

  33. Purification of DNA-Templated Reactions Purification with scarless or useful scar linker A B A A B B A B B A Wash with 4M guanidinium chloride B B B A

  34. Purification of DNA-Templated Reactions Purification with scarless or useful scar linker A B A A B B A B B A Wash with 4M guanidinium chloride B B B B A A

  35. Purification of DNA-Templated Reactions Purification with autocleaving linkers A B A A B B A B B A Wash with 4M guanidinium chloride B B A + A

  36. Multistep Synthesis of Small Molecules 1) NH2 2 3 1 DMT-MM 2) Capture with Avidin beads Wash with 4M guanidinium chloride 3) Cleavage buffer pH = 11.8 4 DMT-MM 5

  37. Multistep Synthesis of Small Molecules 5 6

  38. Multistep Synthesis of Small Molecules 7 6 • DMT-MM • Avidin beads • 33% overall from 3 8

  39. Multistep Synthesis of Small Molecules NaIO4 9 8 pH 8.5

  40. Multistep Synthesis of Small Molecules Self-elution 10 7% overall yield Li, X., Gartner, Z.J., Tse, B.N., Liu, D.R., J. Am. Chem. Soc. 2004, 126, 5090.

  41. Introduction to DTS Organic Reactions in DTS Fundamental reactions, distance dependence and independence New, synthetically useful architectures Example of a Small Molecule Synthesis Synthetic strategies, linkers, purification Towards the Synthesis of Small Molecule Libraries Conclusions

  42. Synthesis of Libraries of Macrocycles • A library of 65 macrocycles was successfully synthesized and screened in one solution. • Each synthetic step carried out in one solution was the same for all templates, only with different reagents. • Would it be possible to perform branching syntheses with several different reaction classes occurring at the same time in the same solution? Gartner, Z.J., Tse, B.N., Grubina, R., Doyon, J.B., Snyder, T.M., Liu, D.R. Science, 2004, 305, 1601.

  43. One-pot, controlled reaction of cross-reactive reagents NH2 SH Calderone, C.T., Puckett, J.W., Gartner, Z.J., Liu, D.R. Angew. Chem. Int. Ed. Engl. 2002, 41, 4104.

  44. One-pot, controlled reaction of cross-reactive reagents EDC, Sulfo-NHS, NaBH3CN SH NH2 Calderone, C.T., Puckett, J.W., Gartner, Z.J., Liu, D.R. Angew. Chem. Int. Ed. Engl. 2002, 41, 4104.

  45. Diversification by Branching Reaction Pathways NH2

  46. Diversification by Branching Reaction Pathways NH2 11 NH2 NH2 12 NH2 13 NH2 Calderone, C., Liu, D.R. Angew. Chem. Int. Ed. 2005, ASAP.

  47. Diversification by Branching Reaction Pathways 11 14 12 15 13 16 Calderone, C., Liu, D.R. Angew. Chem. Int. Ed. 2005, ASAP.

  48. Diversification by Branching Reaction Pathways 8.3% 17 14 18 14 3.6% 15 16 16

  49. Diversification by Branching Reaction Pathways 17 14 18 14 2% 19 15 16 16

  50. Diversification by Branching Reaction Pathways 17 14 18 14 19 15 1.7% 20 16 21 0.8% 16

More Related