Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Efficient discovery of bioactive scaffolds by activity-directed synthesis

Nature Chemistry volume 6, pages 872–876 (2014)Cite this article

Subjects

Abstract

The structures and biological activities of natural products have often provided inspiration in drug discovery. The functional benefits of natural products to the host organism steers the evolution of their biosynthetic pathways. Here, we describe a discovery approach—which we term activity-directed synthesis—in which reactions with alternative outcomes are steered towards functional products. Arrays of catalysed reactions of α-diazo amides, whose outcome was critically dependent on the specific conditions used, were performed. The products were assayed at increasingly low concentration, with the results informing the design of a subsequent reaction array. Finally, promising reactions were scaled up and, after purification, submicromolar ligands based on two scaffolds with no previous annotated activity against the androgen receptor were discovered. The approach enables the discovery, in tandem, of both bioactive small molecules and associated synthetic routes, analogous to the evolution of biosynthetic pathways to yield natural products.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on SpringerLink
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Application of activity-directed synthesis to the discovery of androgen receptor agonists.
Figure 2: Activity of product mixtures derived from reaction arrays.
Figure 3: Dose-dependent agonism of the androgen receptor by compounds 17, 18 and 19.
Figure 4: A selection of the alternative products accessible from α-diazo amides 8, 3 and 13, which were explored in rounds one, two and three.

Similar content being viewed by others

References

  1. Newman, D. J. & Cragg, G. M. Natural products as sources of new drugs over the last 25 years. J. Nat. Prod. 70, 461–477 (2007).

    Article  CAS  Google Scholar 

  2. Beghyn, T., Deprez-Poulain, R., Willand, N., Folleas, B. & Deprez, B. Natural compounds: leads or ideas? Bioinspired molecules for drug discovery. Chem. Biol. Drug Des. 72, 3–15 (2008).

    Article  CAS  Google Scholar 

  3. Wetzel, S., Bon, R. S., Kumar, K. & Waldmann, H. Biology-oriented synthesis. Angew. Chem. Int. Ed. 50, 10800–10826 (2011).

    Article  CAS  Google Scholar 

  4. Maplestone, R. A., Stone, M. J. & Williams, D. H. The evolutionary role of secondary metabolites—a review. Gene 115, 151–157 (1992).

    Article  CAS  Google Scholar 

  5. Firn, R. D. & Jones, C. G. Natural products—a simple model to explain chemical diversity. Nat. Prod. Rep. 20, 382–391 (2003).

    Article  CAS  Google Scholar 

  6. Krier, M., Bret, G. & Rognan, D. Assessing the scaffold diversity of screening libraries. J. Chem. Inf. Model. 46, 512–524 (2006).

    Article  CAS  Google Scholar 

  7. Wetzel, S. et al. Interactive exploration of chemical space with Scaffold Hunter. Nature Chem. Biol. 5, 581–583 (2009).

    Article  CAS  Google Scholar 

  8. Renner, S. et al. Bioactivity-guided mapping and navigation of chemical space. Nature Chem. Biol. 5, 585–592 (2009).

    Article  CAS  Google Scholar 

  9. Kishirsagar, T. (ed.) High-Throughput Lead Optimization in Drug Discovery (CRC, 2008).

    Book  Google Scholar 

  10. Roughley, S. D. & Jordon, A. M. The medicinal chemist's toolbox: an analysis of reactions used in the pursuit of drug candidates. J. Med. Chem. 54, 3451–3479 (2011).

    Article  CAS  Google Scholar 

  11. Cooper, T. W. J., Campbell, I. B. & Macdonald, S. J. F. Factors determining the selection of organic reactions by medicinal chemists and the use of the reactions in arrays (small focused libraries). Angew. Chem. Int. Ed. 49, 8082–8091 (2010).

    Article  CAS  Google Scholar 

  12. Walters, W. P., Green, J., Weiss, J. R. & Murcko, M. A. What do medicinal chemists actually make? A 50-year retrospective. J. Med. Chem. 54, 6405–6416 (2011).

    Article  CAS  Google Scholar 

  13. Lipkus, A. H. et al. Structural diversity of organic chemistry. A scaffold analysis of the CAS registry. J. Org. Chem. 73, 4443–4451 (2008).

    Article  CAS  Google Scholar 

  14. Trabocchi, A. (ed.) Diversity-Oriented Synthesis: Basics and Applications in Organic Synthesis, Drug Discovery and Chemical Biology (Wiley, 2013).

    Book  Google Scholar 

  15. Burke, M. D. & Schreiber, S. L. A planning strategy for diversity-oriented synthesis. Angew. Chem. Int. Ed. 43, 46–58 (2004).

    Article  Google Scholar 

  16. Galloway, W. R. J. D., Isidro-Llobet, A. & Spring, D. R. Diversity-oriented synthesis as a tool for the discovery of novel biologically active small molecules. Nature Commun. 1, 80 (2010).

    Article  Google Scholar 

  17. Umeno, D., Tobias, A. V. & Arnold, F. H., Diversifying carotenoid biosynthetic pathways by directed evolution. Microbiol. Mol. Biol. Rev. 69, 51–78 (2005).

    Article  CAS  Google Scholar 

  18. Lewis, W. G. et al. Click chemistry in situ: acetylcholinesterase as a reaction vessel for the selective assembly of a femtomolar inhibitor from an array of building blocks. Angew. Chem. Int. Ed. 41, 1053–1057 (2002).

    Article  CAS  Google Scholar 

  19. Hirose, T. et al. Observation of the controlled assembly of preclick components in the in situ click chemistry generation of a chitinase inhibitor. Proc. Natl Acad. Sci. USA 110, 15892–15897 (2013).

    Article  CAS  Google Scholar 

  20. Mamidyala S. K. & Finn, M. G. In situ click chemistry: probing the binding landscapes of biological molecules. Chem. Soc. Rev. 39, 1252–1261 (2010).

    Article  CAS  Google Scholar 

  21. Corbett, P. T. et al. Dynamic combinatorial chemistry. Chem. Rev. 106, 3652–3711 (2006).

    Article  CAS  Google Scholar 

  22. Davies, H. M. & Morton, D. Guiding principles for site selective and stereoselective intermolecular C–H functionalization by donor/acceptor rhodium carbenes. Chem. Soc. Rev. 40, 1857–1869 (2011).

    Article  CAS  Google Scholar 

  23. Padwa, A. & Weingarten, D. M. Cascade processes of metallo carbenoids. Chem. Rev. 96, 223–269 (1996).

    Article  CAS  Google Scholar 

  24. Doyle, M. P. & Forbes, D. C. Recent advances in asymmetric catalytic metal carbene transformations. Chem. Rev. 98, 911–935 (1998).

    Article  CAS  Google Scholar 

  25. Davies, H. M. L. & Beckwith, R. E. J. Catalytic enantioselective C–H activation by means of metal–carbenoid-induced C–H insertion. Chem. Rev. 103, 2861–2903 (2003).

    Article  CAS  Google Scholar 

  26. Nadeau, E., Ventura, D. L., Brekan, J. A. & Davies H. M. L. Controlling factors for C–H functionalization versus cyclopropanation of dihydronaphthalenes. J. Org. Chem. 75, 1927–1939 (2010).

    Article  CAS  Google Scholar 

  27. Davies, H. M. L., Matasi, J. J. & Ahmed G. Divergent pathways in the intramolecular reactions between rhodium-stabilized vinylcarbenoids and pyrroles: construction of fused tropanes and 7-azabicyclo[4.2.0]octadienes. J. Org. Chem. 61, 2305–2313 (1996).

    Article  CAS  Google Scholar 

  28. Gao, W., Bohl, C. E. & Dalton, J. T. Chemistry and structural biology of androgen receptor. Chem. Rev. 105, 3352–3370 (2005).

    Article  CAS  Google Scholar 

  29. Fang, H. et al. Study of 202 natural, synthetic, and environmental chemicals for binding to the androgen receptor. Chem. Res. Toxicol. 16, 1338–1358 (2003).

    Article  CAS  Google Scholar 

  30. Gao, W. & Dalton, J. T. Expanding the therapeutic use of androgens via selective androgen receptor modulators (SARMs). Drug Discov. Today 12, 241–248 (2007).

    Article  CAS  Google Scholar 

  31. Mitchell, L. H. et al. Rational design of a topical androgen receptor antagonist for the suppression of sebum production with properties suitable for follicular delivery. J. Med. Chem. 53, 4422–4427 (2010).

    Article  CAS  Google Scholar 

  32. Tong, Y. Androgen receptor antagonists and uses thereof. PCT patent WO 2012119559 A1 (2012).

  33. Gauthier, D., Dodd, R. H. & Dauban, P. Regioselective access to substituted oxindoles via rhodium-catalyzed carbene C–H insertion. Tetrahedron 65, 8542–8555 (2009).

    Article  CAS  Google Scholar 

  34. Ozers, M. S. et al. The androgen receptor T877A mutant recruits LXXLL and FXXLF peptides differently than wild-type androgen receptor in a time-resolved fluorescence resonance energy transfer assay. Biochemistry 46, 683–695 (2007).

    Article  Google Scholar 

  35. Kyranos, J. (ed.) High Throughput Analysis For Early Drug Discovery (Elsevier, 2004).

    Google Scholar 

  36. Cawse, J. N., Wroczynski, S. & Darchun, B. Y. Method for defining an experimental space and method and system for conducting combinatorial high throughput screening of mixtures. US patent 6,826,487 B1 (2004).

  37. Espino, C. G., Fiori, K. W., Kim, M. & Du Bois, J. Expanding the scope of C–H amination through catalyst design. J. Am. Chem. Soc. 126, 15378–15379 (2004).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

The authors acknowledge funding from the University of Leeds and from the EPSRC (for equipment). The authors also thank K. Krishenbaum, P. M. Levine (both New York University) and S. Bartlett (University of Leeds) for discussions.

Author information

Authors and Affiliations

  1. Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK

    George Karageorgis, Stuart Warriner & Adam Nelson

  2. School of Chemistry, University of Leeds, Leeds, LS2 9JT, UK

    George Karageorgis, Stuart Warriner & Adam Nelson

Authors
  1. George Karageorgis
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Stuart Warriner
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Adam Nelson
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

A.N. and S.W. conceived, designed and supervised the project. G.K. undertook the experimental work. A.N., S.W. and G.K. analysed the results and wrote the paper.

Corresponding authors

Correspondence to Stuart Warriner or Adam Nelson.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary information

Supplementary information (PDF 2984 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Karageorgis, G., Warriner, S. & Nelson, A. Efficient discovery of bioactive scaffolds by activity-directed synthesis. Nature Chem 6, 872–876 (2014). https://doi.org/10.1038/nchem.2034

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nchem.2034

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing