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.

  • Perspective
  • Published:

Advances in the use of synthetic combinatorial chemistry: Mixture-based libraries

The conceptual and technical approaches that led to the explosive growth of combinatorial chemistry began approximately 20 years ago. In the past decade, combinatorial chemistry has continued to expand with new chemistries, technological improvements and, most importantly, a clear demonstration of its utility in the identification of active compounds for research and drug-discovery programs. This article describes the conceptual and practical breakthroughs that have been critical for the development of synthetic combinatorial methods and includes the most recent developments and applications of mixture-based combinatorial libraries.

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

Access options

Buy this article

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

Figure 1: Conceptual illustration of a tripeptide PS-SCL (top) and representation of a peptide (middle) and heterocyclic (bottom) PS-SCL.
Figure 2: Elucidation of T-cell specificity and the identification of ligands for the μ-opioid receptor using biometrical analysis.

References

  1. Merrifield, R.B. Peptide synthesis. I. The synthesis of a tetrapeptide. J. Am. Chem. Soc. 85, 2149–2154 (1963).

    Article  CAS  Google Scholar 

  2. Merrifield, R.B. Solid-phase synthesis. Science 232, 341–347 (1986).

    Article  CAS  Google Scholar 

  3. Frank, R. A new general approach for the simultaneous chemical synthesis of large numbers of oligonucleotides: segmental solid supports. Nucleic Acids Res. 11, 4365–4377 (1983).

    Article  CAS  Google Scholar 

  4. Geysen, H.M., Meloen, R.H. & Barteling, S.J. Use of a peptide synthesis to probe viral antigens for epitopes to a resolution of a single amino acid. Proc. Natl. Acad. Sci. USA 81, 3998–4002 (1984).

    Article  CAS  Google Scholar 

  5. Houghten, R.A. General method for the rapid solid-phase synthesis of large numbers of peptides: specificity of antigen–antibody interaction at the level of individual amino acids. Proc. Natl. Acad. Sci. USA 82, 5131–5135 (1985).

    Article  CAS  Google Scholar 

  6. Leznoff, C.C. & Wong, J.Y. The use of polymer supports in organic synthesis III. Selective chemical reactions on one aldehyde group of symmetrical dialdehydes. Can. J. Chem. 51, 3756–3764 (1973).

    Article  CAS  Google Scholar 

  7. Wong, J.Y. & Leznoff, C.C. The use of polymer supports in organic synthesis II. The syntheses of monoethers of symmetrical diols. Can. J. Chem. 51, 2452–2456 (1973).

    Article  CAS  Google Scholar 

  8. Crowley, J.I. & Rapoport, H. Solid-phase organic synthesis: Novelty or fundamental concept? Acc. Chem. Res. 9, 135–144 (1976).

    Article  CAS  Google Scholar 

  9. Bunin, B.A. & Ellman, J.A. A general and expedient method for the solid-phase synthesis of 1,4-benzodiazepine derivatives. J. Am. Chem. Soc. 114, 10997–10998 (1992).

    Article  CAS  Google Scholar 

  10. Thompson, L.A. & Ellman, J.A. Synthesis and applications of small molecule libraries. Chem. Rev. 96, 555–600 (1996).

    Article  CAS  Google Scholar 

  11. Nefzi, A., Ostresh, J.M. & Houghten, R.A. The current status of heterocyclic combinatorial libraries. Chem. Rev. 97, 449–472 (1997).

    Article  CAS  Google Scholar 

  12. Dolle, R.E. Comprehensive survey of combinatorial library synthesis: 2000. J. Comb. Chem. 3, 477–517 (2001).

    Article  CAS  Google Scholar 

  13. Bunin, B.A., Plunkett, M.J. & Ellman, J.A. The combinatorial synthesis and chemical and biological evaluation of a 1,4-benzodiazepine library. Proc. Natl. Acad. Sci. USA 91, 4708–4712 (1994).

    Article  CAS  Google Scholar 

  14. Ostresh, J.M. et al. Solid-phase synthesis of trisubstituted bicyclic guanidines via cyclicization of reduced N-acylated dipeptides. J. Org. Chem. 63, 8622–8623 (1998).

    Article  CAS  Google Scholar 

  15. Ostresh, J.M. et al. “Libraries from libraries”: chemical transformation of combinatorial libraries to extend the range and repertoire of chemical diversity. Proc. Natl. Acad. Sci. USA 91, 11138–11142 (1994).

    Article  Google Scholar 

  16. Giannis, A. & Kolter, T. Peptidomimetics for receptor ligands—Discovery, development, and medical perspectives. Angew. Chem. Int. Ed. Engl. 32, 1244–1267 (1993).

    Article  Google Scholar 

  17. Liskamp, R.M.J. Opportunities for new chemical libraries: Unnatural biopolymers and diversomers. Angew. Chem. Int. Ed. Engl. 33, 633–636 (1994).

    Article  Google Scholar 

  18. Barkley, A. & Arya, P. Combinatorial chemistry toward understanding the function(s) of carbohydrates and carbohydrate conjugates. Chemistry 7, 555–563 (2001).

    Article  CAS  Google Scholar 

  19. Lam, K.S. et al. A new type of synthetic peptide library for identifying ligand-binding activity. Nature 354, 82–84 (1991).

    Article  CAS  Google Scholar 

  20. Houghten, R.A. et al. Generation and use of synthetic peptide combinatorial libraries for basic research and drug discovery. Nature 354, 84–86 (1991).

    Article  CAS  Google Scholar 

  21. Hiemstra, H.S. et al. The identification of CD4+ T cell epitopes with dedicated synthetic peptide libraries. Proc. Natl. Acad. Sci. USA 94, 10313–10318 (1997).

    Article  CAS  Google Scholar 

  22. Pinilla, C., Appel, J.R., Blanc, P. & Houghten, R.A. Rapid identification of high affinity peptide ligands using positional scanning synthetic peptide combinatorial libraries. Biotechniques 13, 901–905 (1992).

    CAS  PubMed  Google Scholar 

  23. Houghten, R.A. et al. Mixture-based synthetic combinatorial libraries. J. Med. Chem. 42, 3743–3778 (1999).

    Article  CAS  Google Scholar 

  24. Geysen, H.M., Rodda, S.J. & Mason, T.J. A priori delineation of a peptide which mimics a discontinuous antigenic determinant. Mol. Immunol. 23, 709–715 (1986).

    Article  CAS  Google Scholar 

  25. Lam, K.S., Lebl, M. & Krchnak, V. The “one-bead-one-compound” combinatorial library method. Chem. Rev. 97, 411–448 (1997).

    Article  CAS  Google Scholar 

  26. Ohlmeyer, M.H.J. et al. Complex synthetic chemical libraries indexed with molecular tags. Proc. Natl. Acad. Sci. USA 90, 10922–10926 (1993).

    Article  CAS  Google Scholar 

  27. Houghten, R.A. Soluble combinatorial libraries: extending the range and repertoire of chemical diversity. Methods: Companion Methods Enzymol. 6, 354–360 (1994).

    Article  CAS  Google Scholar 

  28. Berman, J., Halm, K., Adkison, K. & Shaffer, J. Simultaneous pharmacokinetic screening of a mixture of compounds in the dog using API LC/MS/MS analysis for increased throughput. J. Med. Chem. 40, 827–829 (1997).

    Article  CAS  Google Scholar 

  29. Cheng, Y. et al. A combinatorial library of indinavir analogues and its in vitro and in vivo studies. Bioorg. Med. Chem. Lett. 12, 529–532 (2002).

    Article  CAS  Google Scholar 

  30. Thornberry, N.A. et al. A combinatorial approach defines specificities of members of the caspase family and granzyme B—Functional relationships established for key mediators of apoptosis. J. Biol. Chem. 272, 17907–17911 (1997).

    Article  CAS  Google Scholar 

  31. Rano, T.A. et al. A combinatorial approach for determining protease specificities: application to interleukin-1β converting enzyme (ICE). Chem. Biol. 4, 149–155 (1997).

    Article  CAS  Google Scholar 

  32. Backes, B.J., Harris, J.L., Leonetti, F., Craik, C.S. & Ellman, J.A. Synthesis of positional-scanning libraries of fluorogenic peptide substrates to define the extended substrate specificity of plasmin and thrombin. Nature Biotechnol. 18, 187–193 (2000).

    Article  CAS  Google Scholar 

  33. Harris, J.L. et al. Rapid and general profiling of protease specificity by using combinatorial fluorogenic substrate libraries. Proc. Natl. Acad. Sci. USA 97, 7754–7759 (2000).

    Article  CAS  Google Scholar 

  34. Harris, J.L. et al. Definition of the extended substrate specificity determinants for β-tryptases I and II. J. Biol. Chem. 276, 34941–34947 (2001).

    Article  CAS  Google Scholar 

  35. Salter, J.P. et al. Cercarial elastase is encoded by a functionally conserved gene family across multiple species of schistosomes. J. Biol. Chem. 277, 24618–24624 (2002).

    Article  CAS  Google Scholar 

  36. Mathieu, M.A. et al. Substrate specificity of schistosome versus human legumain determined by P1-P3 peptide libraries. Mol. Biochem. Parasitol. 121, 99–105 (2002).

    Article  CAS  Google Scholar 

  37. Dauber, D.S. et al. Altered substrate specificity of drug-resistant human immunodeficiency virus type 1 protease. J. Virol. 76, 1359–1368 (2002).

    Article  CAS  Google Scholar 

  38. Nazif, T. & Bogyo, M. Global analysis of proteasomal substrate specificity using positional-scanning libraries of covalent inhibitors. Proc. Natl. Acad. Sci. USA 98, 2967–2972 (2001).

    Article  CAS  Google Scholar 

  39. Harris, J.L., Alper, P.B., Li, J., Rechsteiner, M. & Backes, B.J. Substrate specificity of the human proteasome. Chem. Biol. 8, 1131–1141 (2001).

    Article  CAS  Google Scholar 

  40. Nefzi, A., Giulianotti, M.A. & Houghten, R.A. Solid-phase synthesis of substituted 2,3-diketopiperazines from reduced polyamides. Tetrahedron 56, 3319–3326 (2000).

    Article  CAS  Google Scholar 

  41. Acharya, A.N., Nefzi, A., Ostresh, J.M. & Houghten, R.A. Tethered libraries: solid-phase synthesis of substituted urea-linked bicyclic guanidines. J. Comb. Chem. 3, 189–195 (2001).

    Article  CAS  Google Scholar 

  42. Pinilla, C., Appel, J.R. & Houghten, R.A. Investigation of antigen-antibody interactions using a soluble nonsupport-bound synthetic decapeptide library composed of four trillion sequences. Biochem. J. 301, 847–853 (1994).

    Article  CAS  Google Scholar 

  43. Udaka, K., Wiesmüller, K.-H., Kienle, S., Jung, G. & Walden, P. Self-MHC-restricted peptides recognized by an alloreactive T lymphocyte clone. J. Immunol. 157, 670–678 (1996).

    CAS  PubMed  Google Scholar 

  44. Hemmer, B. et al. Identification of high potency microbial and self ligands for a human autoreactive class II-restricted T cell clone. J. Exp. Med. 185, 1651–1659 (1997).

    Article  CAS  Google Scholar 

  45. Pinilla, C. et al. Exploring immunological specificity using synthetic peptide combinatorial libraries. Curr. Opin. Immunol. 11, 193–202 (1999).

    Article  CAS  Google Scholar 

  46. Hemmer, B. et al. Identification of candidate T cell epitopes and molecular mimics in chronic Lyme disease. Nature Med. 5, 1375–1382 (1999).

    Article  CAS  Google Scholar 

  47. Zhao, Y. et al. Combinatorial peptide libraries and biometric score matrices permit the quantitative analysis of specific and degenerate interactions between clonotypic TCR and MHC peptide ligands. J. Immunol. 167, 2130–2141 (2001).

    Article  CAS  Google Scholar 

  48. La Rosa, C. et al. Enhanced immune activity of cytotoxic T-lymphocyte epitope analogs derived from positional scanning synthetic combinatorial libraries. Blood 97, 1776–1786 (2001).

    Article  CAS  Google Scholar 

  49. Hemmer, B. et al. Contribution of individual amino acids within MHC molecule or antigenic peptide to TCR ligand potency. J. Immunol. 164, 861–871 (2000).

    Article  CAS  Google Scholar 

  50. Anderson, B., Park, B.J., Verdaguer, J., Amrani, A. & Santamaria, P. Prevalent CD8+ T cell response against one peptide/MHC complex in autoimmune diabetes. Proc. Natl. Acad. Sci. USA 96, 9311–9316 (1999).

    Article  CAS  Google Scholar 

  51. Judkowski, V. et al. Identification of MHC class II-restricted peptide ligands, including a glutamic acid decarboxylase 65 sequence, that stimulate diabetogenic T cells from transgenic BDC2.5 nonobese diabetic mice. J. Immunol. 166, 908–917 (2001).

    Article  CAS  Google Scholar 

  52. Pinilla, C. et al. Combinatorial peptide libraries as an alternative approach to the identification of ligands for tumor reactive cytolytic T lymphocytes. Cancer Res. 61, 5153–5160 (2001).

    CAS  PubMed  Google Scholar 

  53. Rubio-Godoy, V. et al. Combinatorial peptide library based identification of peptide ligands for tumor-reactive cytolytic T lymphocytes of unknown specificity. Eur. J. Immunol. 32, 2292–2299 (2002).

    Article  CAS  Google Scholar 

  54. Linnemann, T. et al. Mimotopes for tumor-specific T lymphocytes in human cancer determined with combinatorial peptide libraries. Eur. J. Immunol. 31, 156–165 (2001).

    Article  CAS  Google Scholar 

  55. Rubio-Godoy, V. et al. Towards synthetic combinatorial peptide libraries in positional scanning format (PS-SCL)-based identification of CD8+ tumor-reactive T-cell ligands: A comparative analysis of PS-SCL recognition by a single tumor-reactive CD8+ CTL. Cancer Res. 62, 2058–2063 (2002).

    CAS  PubMed  Google Scholar 

  56. Borras, E. et al. Findings on T cell specificity revealed by synthetic combinatorial libraries. J. Immunol. Methods 267, 79–97 (2002).

    Article  CAS  Google Scholar 

  57. Dooley, C.T. & Houghten, R.A. The use of positional scanning synthetic peptide combinatorial libraries for the rapid determination of opioid receptor ligands. Life Sci. 52, 1509–1517 (1993).

    Article  CAS  Google Scholar 

  58. Reixach, N., Crooks, E., Ostresh, J.M., Houghten, R.A. & Blondelle, S.E. Inhibition of β-amyloid-induced neurotoxicity by imidazopyridoindoles derived from a synthetic combinatorial library. J. Struct. Biol. 130, 247–258 (2000).

    Article  CAS  Google Scholar 

  59. Blondelle, S.E., Crooks, E., Ostresh, J.M. & Houghten, R.A. Mixture-based heterocyclic combinatorial positional scanning libraries: discovery of bicyclic guanidines having potent antifungal activities against Candida albicans and Cryptococcus neoformans. Antimicrob. Agents Chemother. 43, 106–114 (1999).

    Article  CAS  Google Scholar 

  60. Boger, D.L., Fink, B.E. & Hedrick, M.P. Total synthesis of distamycin A and 2640 analogs: A solution-phase combinatorial approach to the discovery of new, bioactive DNA binding agents and development of a rapid, high-throughput screen for determining relative DNA binding affinity or DNA binding sequence selectivity. J. Am. Chem. Soc. 122, 6382–6394 (2000).

    Article  CAS  Google Scholar 

  61. Willoughby, C.A. et al. Combinatorial synthesis of 3-(amidoalkyl) and 3-(aminoalkyl)-2-arylindole derivatives: discovery of potent ligands for a variety of G-protein coupled receptors. Bioorg. Med. Chem. Lett. 12, 93–96 (2002).

    Article  CAS  Google Scholar 

  62. Appel, J.R., Johnson, J., Narayanan, V.L. & Houghten, R.A. Identification of novel antitumor agents from mixture-based synthetic combinatorial libraries using cell-based assays. Mol. Divers. 4, 91–102 (1999).

    Article  CAS  Google Scholar 

  63. Sternson, S.M., Wong, J.C., Grozinger, C.M. & Schreiber, S.L. Synthesis of 7200 small molecules based on a substructural analysis of the histone deacetylase inhibitors trichostatin and trapoxin. Org. Lett. 3, 4239–4242 (2001).

    Article  CAS  Google Scholar 

  64. McMillan, K. et al. Allosteric inhibitors of inducible nitric oxide synthase dimerization discovered via combinatorial chemistry. Proc. Natl. Acad. Sci. USA 97, 1506–1511 (2000).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank R. Martin and R. Simon for their contributions to the development of the biometrical analysis first used in T-cell studies; C. Dooley for the opioid receptor research; D. Wilson and S. Blondelle for their involvement in the use of combinatorial libraries in many different biological assays; and J. Ostresh, A. Nefzi and the chemistry group at Torrey Pines Institute for Molecular Studies for the continuing development of synthetic chemistry for the preparation of mixture-based combinatorial libraries. Supported by NCI grant PO1 CA78040, NIDA grant RO1 DA09410 and MSNRI funding.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Richard A. Houghten.

Supplementary information

Rights and permissions

Reprints and permissions

About this article

Cite this article

Pinilla, C., Appel, J., Borràs, E. et al. Advances in the use of synthetic combinatorial chemistry: Mixture-based libraries. Nat Med 9, 118–122 (2003). https://doi.org/10.1038/nm0103-118

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1038/nm0103-118

This article is cited by

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