Molecular Diversity

, Volume 2, Issue 1–2, pp 29–34 | Cite as

Exploring antibody polyspecificity using synthetic combinatorial libraries

  • Jon R. Appel
  • Jaime Buencamino
  • Richard A. Houghten
  • Clemencia Pinilla
Research Papers


Extensive mapping studies for seven antigen-antibody interactions have been carried out using both individual analogs and peptide libraries. With competitive ELISA, these studies have revealed that monoclonal antibodies exhibit a broad range of specificities, from antibodies that recognize only conservative substitutions for 1–2 positions of the antigenic determinant, to antibodies that recognize sequences that are completely unrelated to the parent antigen with comparable affinities. Synthetic combinatorial libraries, containing millions of peptide sequences, permit a more systematic and rapid evaluation of the extent of multiple-binding specificities of monoclonal antibodies than individual analogs. The peptide libraries used here comprise mixtures of compounds having specifically defined positions and mixture positions. The same diversity of sequences in different formats, which differ by the numbers of positions singularly defined and different locations defined within the sequence, can be examined. Comparison of the screening results, selection criteria of the most active mixtures, and different approaches used for the deconvolution of active individual compounds are discussed. Synthetic combinatorial libraries greatly facilitate the understanding of antigen-antibody interactions at the amino acid level and will assist in the development of improved immunodiagnostics.


Synthetic combinatorial libraries Positional scanning Monoclonal antibodies Polyspecificity 


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  1. 1.
    Christian, R.B., Zuckermann, R.N., Kerr, J.M., Wang, L. and Malcolm, B.A.,Simplified methods for construction, assessment and rapid screening of peptide libraries in bacteriophage, J. Mol. Biol., 227 (1992) 711–718.Google Scholar
  2. 2.
    Felici, F., Castagnoli, L., Musacchio, A., Jappelli, R. and Cesareni, G.,Selection of antibody ligands from a large library of oligopeptides expressed on a multivalent exposition vector, J. Mol. Biol., 222 (1991) 301–310.Google Scholar
  3. 3.
    Needels, M.C., Jones, D.G., Tate, E.H., Heinkel, G.L., Kochersperger, L.M., Dower, W.J., Barrett, R.W. and Gallop, M.A.,Generation and screening of an oligonucleotide-encoded synthetic peptide library, Proc. Natl. Acad. Sci. USA, 90 (1993) 10700–10704.Google Scholar
  4. 4.
    Scott, J.K. and Smith, G.P.,Searching for peptide ligands with an epitope library, Science, 249 (1990) 386–390.Google Scholar
  5. 5.
    Pinilla, C., Buencamino, J., Appel, J.R., Hopp, T.P. and Houghten, R.A.,Mapping the detailed specificity of a calcium-dependent monoclonal antibody through the use of soluble positional scanning combinatorial libraries: Identification of potent calcium-independent antigens, Mol. Diversity, 1 (1995) 21–28.Google Scholar
  6. 6.
    Pinilla, C., Buencamino, J., Appel, J.R., Houghten, R.A., Brassard, J.A. and Ruggeri, Z.M.,Two antipeptide monoclonal antibodies that recognize adhesive sequences in fibrinogen: Identification of antigenic determinants and unrelated sequences using synthetic combinatorial libraries, Biomed. Pept. Protein Nucleic Acids, 1 (1995) 199–204.Google Scholar
  7. 7.
    Pinilla, C., Chendra, S., Appel, J.R. and Houghten, R.A.,Elucidation of monoclonal antibody polyspecificity using synthetic combinatorial library, Pept. Res., 8 (1995) 250–257.Google Scholar
  8. 8.
    Van Regenmortel, M.H.V.,Transcending the structuralist paradigm in immunologyaffinity and biological activity rather than purely structural considerations should guide the design of synthetic peptide epitopes, Biomed. Pept. Protein Nucleic Acids, 1 (1995) 109–116.Google Scholar
  9. 9.
    Pinilla, C., Appel, J., Blondelle, S.E., Dooley, C.T., Dörner, B., Eichler, J., Ostresh, J.M. and Houghten, R.A.,A review of the utility of peptide combinatorial libraries, Biopolym. Pept. Sci. Sect., 37 (1995) 221–240.Google Scholar
  10. 10.
    Houghten, R.A., Pinilla, C., Blondelle, S.E., Appel, J.R., Dooley, C.T. and Cuervo, J.H.,Generation and use of synthetic peptide combinatorial libraries for basic research and drug discovery, Nature, 354 (1991) 84–86.Google Scholar
  11. 11.
    Pinilla, C., Appel, J.R., Blanc, P. and Houghten, R.A.,Rapid identification of high-affinity peptide ligands using positional scanning synthetic peptide combinatorial libraries, Biotechniques, 13 (1992) 901–905.Google Scholar
  12. 12.
    Ostresh, J.M., Winkle, J.H., Hamashin, V.T. and Houghten, R.A.,Peptide libraries: Determination of relative reaction rates of protected amino acids in competitive couplings, Biopolymers, 34 (1994) 1681–1689.Google Scholar
  13. 13.
    Dooley, C.T. and Houghten, R.A.,The use of positional scanning synthetic peptide combinatorial libraries for the rapid determination of opioid receptor ligands, Life Sci., 52 (1993) 1509–1517.Google Scholar
  14. 14.
    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 (1985) 5131–5135.Google Scholar
  15. 15.
    Pinilla, C., Appel, J.R. and Houghten, R.A.,Functional importance of amino acid residues making up peptide antigenic determinants, Mol. Immunol., 30 (1993) 577–585.Google Scholar
  16. 16.
    Pinilla, C., Appel, J.R. and Houghten, R.A.,Identification of antigenic determinants using synthetic peptide combinatorial libraries, In Coligan, J.E., Kruisbeek, A.M., Margulies, D.H., Shevach, E.M. and Strober, W. (Eds.) Current Protocols in Immunology, Wiley, New York, NY, U.S.A., 1994, pp. 9.8.1–9.8.15.Google Scholar
  17. 17.
    Appel, J.R., Muller, S., Benkirane, N., Houghten, R.A. and Pinilla, C.,Highly specific, crossreactive sequences recognized by an anti-HBsAg antibody identified from a positional scanning synthetic combinatorial library, Pept. Res., (1996) in press.Google Scholar
  18. 18.
    Appel, J.R., Pinilla, C., Niman, H. and Houghten, R.A.,Elucidation of discontinuous linear determinants in peptides, J. Immunol., 144 (1990) 976–983.Google Scholar
  19. 19.
    Appel, J.R., Buencamino, J., Houghten, R.A. and Pinilla, C.,Mapping the specificity of an antibody against an oncogenic sequence using peptide combinatorial libraries and substitution analogs: Implications for breast cancer detection, In Kaumaya, P.T.P. and Hodges, R.S. (Eds.) Peptides: Chemistry, Structure and Biology (Proceedings of the 14th American Peptide Symposium), Mayflower Scientific Ltd., Kingswinford, U.K., 1996, pp. 794–795.Google Scholar
  20. 20.
    Pinilla, C., Appel, J.R. and Houghten, R.A.,Synthetic peptide combinatorial libraries (SPCLs): Identification of the antigenic determinant of β-endorphin recognized by monoclonal antibody 3 E7, Gene, 128 (1993) 71–76.Google Scholar
  21. 21.
    Pinilla, C., Appel, J.R., Blondelle, S.E., Dooley, C.T., Eichler, J., Ostresh, J.M. and Houghten, R.A.,Versatility of positional scanning synthetic combinatorial libraries for the identification of individual compounds, Drug Dev. Res., 33 (1994) 133–145.Google Scholar
  22. 22.
    Appel, J.R., Pinilla, C. and Houghten, R.A.,Identification of related peptides recognized by a monoclonal antibody using a synthetic peptide combinatorial library, Immunomethods, 1 (1992) 17–23.Google Scholar
  23. 23.
    Getzoff, E.D., Tainer, J.A., Lerner, R.A. and Geysen, H.M.,The chemistry and mechanism of antibody binding to protein antigens, Adv. Immunol., 43 (1988) 1–98.Google Scholar
  24. 24.
    Geysen, H.M., Mason, T.J. and Rodda, S.J.,Cognitive features of continuous antigenic determinants, J. Mol. Recog., 2 (1989) 32–49.Google Scholar
  25. 25.
    Rini, J.M., Schulze-Gahmen, U. and Wilson, I.A.,Structural evidence for induced fit as a mechanism for antibody-antigen recognition, Science, 255 (1992) 959–965.Google Scholar
  26. 26.
    Churchill, M.E.A., Stura, E., Pinilla, C., Appel, J.R., Houghten, R.A., Kono, D.H., Balderas, R.S., Fieser, G.G., Schulze-Gahmen, U. and Wilson, I.A.,Crystal structure of a peptide complex of antiinfluenza peptide antibody Fab 26/9: Comparison of two different antibodies bound to the same peptide antigen, J. Mol. Biol., 241 (1994) 534–556.Google Scholar
  27. 27.
    Ostresh, J.M., Husar, G.M., Blondelle, S.E., Dörner, B., Weber, P.A. and Houghten, R.A.,‘Libraries from libraries’: Chemical transformation of combinatorial libraries to extend the range and repertoire of chemical diversity, Proc. Natl. Acad. Sci. USA, 91 (1994) 11138–11142.Google Scholar
  28. 28.
    Dooley, C.T. and Houghten, R.A.,Identification of μ-selective polyamine antagonists from a synthetic combinatorial library, Analgesia, 1 (1995) 400–404.Google Scholar
  29. 29.
    Eichler, J., Appel, J.R., Blondelle, S.E., Dooley, C.T., Dörner, B., Ostresh, J.M., Pérez-Payá, E., Pinilla, C. and Houghten, R.A.,Peptide, peptidomimetic and organic synthetic combinatorial libraries, Med. Res. Rev., 15 (1995) 481–496.Google Scholar

Copyright information

© ESCOM Science Publishers B.V. 1996

Authors and Affiliations

  • Jon R. Appel
    • 1
  • Jaime Buencamino
    • 1
  • Richard A. Houghten
    • 1
  • Clemencia Pinilla
    • 1
  1. 1.Torrey Pines Institute for Molecular StudiesSan DiegoUSA

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