Encoded library synthesis using chemical ligation and the discovery of sEH inhibitors from a 334-million member library

Scientific Reports

Volumn 5, Issue , 2015, Pages

  Litovchick, Alexander ^a   Dumelin, Christoph E ^b   Habeshian, Sevan ^a   Gikunju, Diana ^a   Guié, Marie Aude ^a   Centrella, Paolo ^a   Zhang, Ying ^a   Sigel, Eric A ^a   Cuozzo, John W ^a   Keefe, Anthony D ^a   Clark, Matthew A ^a  

^a X Chem Incorporated   (United States)

^b NOVARTIS PHARMA AG   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

MOLECULAR LIBRARY; OLIGONUCLEOTIDE;

CHEMISTRY; DRUG DEVELOPMENT; GENE LIBRARY; GENETICS; MOLECULAR LIBRARY; PROCEDURES;

DRUG DISCOVERY; GENE LIBRARY; OLIGONUCLEOTIDES; SMALL MOLECULE LIBRARIES;

EID: 84931282152     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep10916     Document Type: Article

References (30)

1. A Handbook for DNA-Encoded Chemistry (Ed: R. Goodnow) Wiley, Hoboken, NJ, 2014
2. Clark, M. A. Selecting chemicals: the emerging utility of DNA-encoded libraries. Curr. Opin. Chem. Biol. 14, 396-403 (2010).
3. Kleiner, R. E., Dumelin, C. E. & Liu, D. R. Small-molecule discovery from DNA-encoded chemical libraries. Chem. Soc. Rev. 40, 5707-5717 (2011).
4. Franzini, R. M., Neri, D. & Scheurmann J. DNA-encoded chemical libraries: advancing beyond conventional small-molecule libraries. Acc. Chem. Res. 47, 1247-1255 (2014).
5. Gilmartin, A. G. et al. Allosteric Wip1 phosphatase inhibition through fap-subdomain interaction. Nat. Chem. Biol. 10, 181-187 (2014).
6. Kollmann, C. S. et al. Application of encoded library technology (ELT) to a protein-protein interaction target: Discovery of a potent class of integrin lymphocyte function-associated antigen 1 (LFA-1) antagonists. Bioorg. Med. Chem. 22, 2353-2365 (2014).
7. Deng, H. et al. Discovery of highly potent and selective small molecule ADAMTS-5 inhibitors that inhibit human cartilage degradation via encoded library technology (ELT). J. Med. Chem. 55, 7061-79 (2012).
8. Encinas, L. et al. Encoded library technology as a source of hits for the discovery and lead optimization of a potent and selective class of bactericidal direct inhibitors of Mycobacterium tuberculosis InhA. J. Med. Chem. 57, 1276-88 (2014).
9. Disch, J. S. et al. Discovery of thieno[3, 2-d]pyrimidine-6-carboxamides as potent inhibitors of SIRT1, SIRT2, and SIRT3. J. Med. Chem. 56, 3666-79 (2013).
10. Gentile, G. et al. 5-Aryl-4-carboxamide-1, 3-oxazoles: potent and selective GSK-3 inhibitors. Bioorg. Med. Chem. Lett. 22, 1989-94 (2012).
11. Needels, M. C. et al. Generation and screening of an oligonucleotide-encoded synthetic peptide library. Proc. Natl. Acad. Sci. USA 90, 10700-10704 (1993).
12. Brenner, S. & Lerner, R. A. Encoded combinatorial chemistry. Proc. Natl. Acad. Sci. USA 89, 5381-5383 (1992).
13. Kinoshita, Y. & Nishigaki, K. Enzymatic synthesis of code regions for encoded combinatorial chemistry (ECC). Nucl. Acids Symp. S e r. 34, 201-202 (1995).
14. Clark, M.A. et al. Design, synthesis and selection of DNA-encoded small-molecule libraries. Nat. Chem. Biol. 5, 647-654 (2009).
15. Buller, F., Mannocci, L., Zhang, Y., Dumelin, C. E., Scheurmann, J. & Neri, D. Design and synthesis of a novel DNA-encoded chemical library using Diels-Alder cycloadditions. Bioorg. Med. Chem. Lett. 18, 5926-5931 (2008).
16. El-Sagheer, A. H. & Brown, T. Synthesis and polymerase chain reaction amplifcation of DNA strands containing an unnatural triazole linkage. J. Am. Chem. Soc. 131, 3958-3964 (2009).
17. El-Sagheer, A. H., Sanzone, A. P., Gao, R., Tavassoli, A. & Brown, T. Biocompatible artifcial DNA linker that is read through by DNA polymerases and is functional in Escherichia coli. Proc. Natl. Acad. Sci. USA 28, 11338-11343 (2011).
18. Sanzone, A. P., El-Sagheer, A. H., Brown, T. & Tavassoli, A. Assessing the biocompatibility of click-linked DNA in Escherichia coli. Nucl. Acids Res. 40, 10567-10575 (2012).
19. Birts, C. N., Sanzone, A. P., El-Sagheer, A. H., Blaydes, J. P., Brown, T. & Tavassoli, A. Transcription of click-linked DNA in human cells. Angew. Chem. Int. Ed. 53, 2362-2365 (2014).
20. Litovchick, A., Clark, M. A. & Keefe, A. D. Universal strategies for the DNA-encoding of libraries of small molecules using the chemical ligation of oligonucleotide tags. Artifcial DNA: PNA & XNA 5, e27896 (2014).
21. Gramlich, P. M., Warncke S., Gierlich, J. & Carell, T. Click-click-click: single to triple modifcation of DNA. Angew. Chem. Int. Ed. 47, 3442-344 (2008).
22. Omuni, A., Beach, D. G., Baker, M., Gabryelski, W. & Manderville, R. A. Postsynthetic Guanine Arylation of DNA by Suzuki-Miyaura Cross-Coupling J. Am. Chem. Soc. 133, 42-50 (2011).
23. Lercher, L., McGouran, J. F., Kessler, B. M., Schofeld, C. J. & Davis, B. D. Angew. Chem Int. Ed. 52, 10553-10558 (2013).
24. Ding, Y. & Clark, M. A. Robust Suzuki-Miyaura Cross-Coupling on DNA-Linked Substrates ACS Comb. Sci. 2014, ASAP Nov. 2014.
25. Perissutti, E. et al. Design and synthesis of potential β-sheet nucleators via Suzuki coupling reaction. Tetrahedron 63, 12779-12785 (2007).
26. Karig, G., Spencer, J. A. & Gallagher, T. Directed deprotonation-transmetalation as a route to substituted pyridines. Org. Lett. 3, 835-838 (2001).
27. Miyaura, N., Ishiyama, T., Sasaki, H., Ishikawa, M., Satoh, M. & Suzuki, A. Palladium-catalyzed inter-and intramolecular cross-coupling reactions of B-alkyl-9-borabicyclo[3.3.1]nonane derivatives with 1-halo-1-alkenes or haloarenes. Syntheses of functionalized alkenes, arenes, and cycloalkenes via a hydroboration-coupling sequence. J. Am. Chem. Soc. 111, 314-321 (1989).
28. Podolin, P. L. et al. In vitro and in vivo characterization of a novel soluble epoxide hydrolase inhibitor. Prostaglandins Other Lipid Mediators 104-105, 25-31 (2013).
29. Talji, R. K. et al. Discovery of 1-(1, 3, 5-triazin-2-yl)piperidine-4-carboxamides as inhibitors of soluble epoxide hydrolase. Bioorg. Med. Chem. Lett. 23, 3584-3588 (2013).
30. Keefe, A.D., Clark, M.A., Hupp, C.D., Litovchick, A., Zhang, Y. Chemical ligation methods for the tagging of DNA-encoded chemical libraries. Curr Opin Chem Biol. 26, 80-88 (2015).