Soluble synthetic combinatorial libraries: The use of molecular diversities for drug discovery

Combinatorial Libraries: Synthesis, Screening and Application Potential

Volumn , Issue , 2013, Pages 1-26

  Dörner, Barbara ^a   Blondelle, Sylvie E ^a   Pinilla, Clemencia ^a   Appel, Jon ^a   Dooley, Colette T ^a   Eichler, Jutta ^a   Ostresh, John M ^a   Pérez Payá, Enrique ^a   Houghten, Richard A ^a  

^a TORREY PINES INSTITUTE FOR MOLECULAR STUDIES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 85067220609     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1515/9783110808902.1     Document Type: Chapter

References (66)

1. Appel, J.R., Pinilla, C., and HouGhten, R.A. (1992). Identification of related peptides recoGnized by a monoclonal antibody usinG a synthetic peptide combinatorial library. Immunomethods 1,17-23.
2. Appel, J.R., Buencamino, J., HouGhten, R. A., and Pinilla, C. (1995). Study of peptide-antibody interactions usinG a decapeptide positional scanninG library. In: Peptides 94: ProceedinGs of the 23rd European Peptide Symposium, H.L.S. Maia, ed. (Leiden: Escom), pp. 815-816.
3. BlaKe, J., and Litzidavis, L. (1992). Evaluation of peptide libraries - an iterative strateGy to analyze the reactivity the reactivity of peptide mixtures with antibodies. BioconjuGate Chem. 3,510-513.
4. Blondelle, S.E., and HouGhten, R.A. (1992). DesiGn of model peptides havinG potent antimicrobial activities. Biochemistry 31,12688-12694.
5. Blondelle, S.E., and HouGhten, R.A. (1994). Membrane protectinG sequences and new antimicrobial peptides identified throuGh the screeninG of synthetic peptide combinatorial libraries. In: Techniques in Protein Chemistry V, J. W. Crabb, ed. (Orlando: Academic Press), pp. 509-516.
6. Blondelle, S.E., TaKahashi, E., Weber, P.A., and HouGhten, R.A. (1994). Identification of antimicrobial peptides usinG combinatorial libraries made up of unnatural amino acids. Antimicrob. AGents Chemother. 38, 2280-2286.
7. Blondelle, S.E., Pérez-Payá, E., Dooley, C.T., Pinilla, C., and HouGhten, R.A. (1995a). Chemical combinatorial libraries, peptidomimetics and peptide diversity. Trends Anal. Chem. 14, 83-92.
8. Blondelle, S.E., TaKahashi, E., HouGhten, R. A., and Pérez-Payá, E. (1995b) DesiGn of conformationally defined combinatorial libraries. In: Peptides 94: ProceedinGs of the 23rd European Peptide Symposium, H.L.S. Maia, ed. (Leiden: Escom), pp. 85-86.
9. Bunin, B.A., PlunKett, M.J., and Ellman, J.A. (1994). The combinatorial synthesis and chemical and bioloGical evaluation of a 1,4-benzodiazepine library. Proc. Natl. Acad. Sci. USA 91,4708-4712.
10. Charpentier, S., SaGan, S., Delfour, A., and Nicolas, P. (1991). DermenKephalin and deltorphin I reveal similarities within liGand-bindinG domains of M- and δ-opioid receptors and an additional address subsite on the d-receptor. Biochem. Biophys. Res. Commun. 179,1161-1168.
11. Cho, Y.C., Moran, E.J., Cherry, S.R., Stephans, J.C., Fodor, S.P.A., Adams, C.L., Sundaram, A., Jacobs, J.W., and Schultz, P. G. (1993). An unnatural biopolymer. Science 261, 1303-1305.
12. Cuervo, J.H., Weitl, F., Ostresh, J.M., Hamashin, V.T., Hannah, A.L., and HouGhten, R. A. (1995). PolyalKylamine chemical combinatorial libraries. In: Peptides 94: ProceedinGs of the 23rd European Peptide Symposium, H.L.S. Maia, ed. (Leiden: Escom), pp. 465-466.
13. Cwirla, S.E., Peters, E.A., Barrett, R.W., and Dower, W.J. (1990). Peptides on phaGe: A vast library of peptides for identifyinG liGands. Proc. Natl. Acad. Sci. USA 87, 6378-6382.
14. DarlaK, K., RomanovsKis, P., and Spatola, A. F. (1994). Cyclic Peptide Libraries. In: Peptides, ProceedinGs of the 13th American Peptide Symposium, R.S. HodGesand J.A. Smith, eds. (Leiden: ESCOM), pp. 981-983.
15. Devlin, J.J., PanGaniban, L.C., and Devlin, P.E. (1990). Random peptide libraries: A source of specific protein bindinG molecules. Science 249,404-406.
16. DeWitt, S. H., Kiely, J. S., StanKovic, C.J., Schroeder, M.C., Cody, D.M.R., and Pavia, M.R. (1993). “Diversomers�?: An approach to nonpeptide, nonoliGomeric chemical diversity. Proc. Natl. Acad. Sci. USA 90, 6909-6913.
17. DiMaio, J., and Schiller, P.W. (1980). A cyclic enKephalin analoG with hiGh in vitro opiate activity. Proc. Natl. Acad. Sci. USA 77, 7162-7166.
18. Dooley, C.T., and HouGhten, R. A. (1993). The use of positional scanninG synthetic peptide combinatorial libraries for the rapid determination of opioid receptor liGands. Life Sciences 52,1509-1517.
19. Dooley, C.T., ChunG, N.N., Schiller, P.W., and HouGhten, R.A. (1993). Acetalins: New opioid receptor antaGonists determined throuGh the use of Synthetic Peptide Combinatorial Libraries. Proc. Natl. Acad. Sci. USA 90,10811-10815.
20. Dooley, C.T., and HouGhten, R.A. (1994). New, potent N-acetylated all D-amino acid opioid peptides. In: Peptides: Chemistry, Structure and BioloGy. ProceedinGs of the 13th American Peptide Symposium, R.S. HodGesand J.A. Smith, eds. (Leiden: Escom), pp. 984-985.
21. Dooley, C.T., Hope, S.K., and HouGhten, R.A. (1995). Identification of tetrameric opioid peptides from a combinatorial library composed of L-, D- and non-proteinoGenic amino acids. In: Peptides 94: ProceedinGs of the 23rd European Peptide Symposium, H.L.S. Maia, ed. (Leiden: Escom), pp. 805-806.
22. Dooley C.T, ChunG N.N, WilKes B.C, Schiller, P.W., BidlacK, J.M., PasternaK, G.W., and HouGhten, R.A. (1994). An all D-amino acid opioid peptide with central analGesic activity from a combinatorial library. Science, 266, 2019-2022.
23. Dörner, B., Ostresh, J. M., Husar, G. M., and HouGhten, R.A. ExtendinG the ranGe of molecular diversity throuGh amide alKylation of peptide libraries. In: Peptides 94: ProceedinGs of the 23rd European Peptide Symposium, H.L.S. Maia, ed. (Leiden: Escom), in press.
24. Eichler, J., and HouGhten, R.A. (1993). Identification of substrate-analoG trypsin inhibitors throuGh the screeninG of synthetic peptide combinatorial libraries. Biochemistry 32, 11035-11041.
25. Eichler, J., LucKa, A. W., and HouGhten, R.A. (1994b). Cyclic peptide template combinatorial libraries: Synthesis and identification of chymotrypsin inhibitors. Pept. Res. 7, 300-307.
26. Eichler, J., Pinilla, C, Chendra, S., Appel, J.R., and HouGhten, R.A. (1994a). Synthesis of peptide libraries on cotton carriers: Methods and applications. In: Innovation and Perspectives in Solid Phase Synthesis - Peptides, Polypeptides and OliGonucleotides, R. Epton, ed. (BirminGham: Mayflower Worldwide Limited), pp. 227-232.
27. Eichler, J., LucKa, A.W., and HouGhten, R.A. (1995). Cyclic peptide template synthetic combinatorial libraries. In: Peptides 94: ProceedinGs of the 23rd European Peptide Symposium, H.L.S. Maia, ed. (Leiden: Escom), pp. 461-462.
28. Fodor, S.P.A., Read, J.L., PirrunG, M.C., Stryer, L., Lu, A.T., and Solas, D. (1991). LiGhtdirected, spatially addressable parallel chemical synthesis. Science 251, 767-773.
29. FurKa, A., Sebestyen, F., AsGedom, M., and Dibo, G. (1991). General method for rapid synthesis of multicomponent peptide mixtures. Int. J. Pept. Protein Res. 37, 487-493.
30. Gallop, M. A., Barrett, R.W., Dower, W.J., Fodor, S. P. A., and Gordon, E.M. (1994). Applications of combinatorial technoloGies to druG discovery. 1. BacKGround and peptide combinatorial libraries. J. Med. Chem. 37,1233-1251.
31. Geysen, H.M., Rodda, S.J., and Mason, T.J. (1986). A priori delineation of a peptide which mimics a discontinuous antiGenic determinant. Mol. Immunol. 23, 709-715.
32. Geysen, H.M., and Mason, T.J. (1993). ScreeninG chemically synthesized peptide libraries for bioloGically-relevant molecules. BioMed. Chem. Lett. 3,397-404.
33. Gordon, E.M., Barrett, R.W., Dower, W.J., Fodor, S.P.A., and Gallop, M.A. (1994). Applications of combinatorial technoloGies to druG discovery. 2. Combinatorial orGanic synthesis, library screeninG strateGies, and future directions. J. Med. Chem. 37,1385-1401.
34. Hortin, G.L., Staatz, W.D., and Santoro, S.A. (1992). Preparation of soluble peptide libraries: Application to studies of platelet adhesion sequences. Biochem. Int. 26, 731-738.
35. HouGhten, R. A. (1985). 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.
36. HouGhten, R.A., Bray, M.K., De Graw, S.T., and Kirby, C.J. (1986). Simplified procedure for carryinG out simultaneous multiple hydroGen fluoride cleavaGes of protected peptide resins. Int. J. Pept. Protein Res. 27, 673-678.
37. HouGhten, R.A., Pinilla, C, Blondelle, S. E., Appel, J.R., Dooley, C.T., and Cuervo, J.H. (1991). Generation and use of synthetic peptide combinatorial libraries for basic research and druG discovery. Nature 354, 84-86.
38. HouGhten, R.A., Appel, J.R., Blondelle, S. E., Cuervo, J. H., Dooley, C.T., and Pinilla, C. (1992). The use of synthetic peptide combinatorial libraries for the identification of bioactive peptides. Biotechniques 13,412-421.
39. HouGhten, R. A., Dinh, K.T., Burcin, D.E., and Blondelle, S.E. (1993). The systematic development of peptides havinG potent antimicrobial activity aGainst E. coli throuGh the use of synthetic peptide combinatorial libraries. In: Techniques in Protein Chemistry IV, R.H. AnGeletti, ed. (Orlando: Academic Press), pp. 249-256.
40. HouGhten, R. A. (1994). FindinG the needle in the haystacK. Curr. Biol. 4,564-567.
41. HouGhten, R. A., Ostresh, J.M., Husar, G.M., Dörner, B., and Blondelle, S.E. (1995). Libraries from libraries: The Generation of peptidomimetic combinatorial diversities. In: Peptides 94: ProceedinGs of the 23rd European Peptide Symposium, H.L.S. Maia, ed. (Leiden: Escom), pp. 459-460.
42. Johnsson, K., Allemann, R.K., Widmer, H., and Benner, S.A. (1993). Synthesis, structure and activity of artificial, rationally desiGned catalytic polypeptides. Nature 365, 530-532.
43. Kerr, J.M., Banville, S.C., and ZucKermann, R.N. (1993). Encoded combinatorial peptide libraries containinG non-natural amino acids. J. Am. Chem. Soc. 115,2529-2531.
44. Lam, K.S., Salmon, S.E., Hersh, E.M., Hruby, V.J., KazmiersKi, W.M., and Knapp, R.J. (1991). A new type of synthetic peptide library for identifyinG liGand-bindinG activity. Nature 354,82-84.
45. Lam, K.S., and Lebl, M. (1992). Streptavidin and avidin recoGnize peptide liGands with different motifs. Immunomethods 1,11-15.
46. Lazarus, L.H., Salvadori, S., SantaGada, V., Tomatis, R., and Wilson, W.E. (1991). Function of neGative charGe in the “Address Domain�? of deltorphins. J. Med. Chem. 34, 1350-1355.
47. 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. (1993). Generation and screeninG of an oliGonucleotide- encoded synthetic peptide library. Proc. Natl. Acad. Sci. USA 90,10700-10704.
48. NiKolaiev, V., Stierandová, A., KrchnáK, V., SeliGmann, B., Lam, K. S., Salmon, S. E., and Lebl, M. (1993). Peptide-encodinG for structure determination of nonsequenceable polymers within libraries synthesized and tested on solid-phase supports. Pept. Res. 6, 161-170.
49. Ohlmeyer, M.H.J., Swanson, R.N., Dillard, L.W., Reader, J.C., Asouline, G., Kobayashi, R., WiGler, M., and Still, W.C. (1993). Complex synthetic chemical libraries indexed with molecular taGs. Proc. Natl. Acad. Sci. USA 90,10922-10926.
50. Ostresh, J.M., Husar, G.M., Blondelle, S.E., Dörner, B., Weber, P.A., and HouGhten, R.A. (1994a). “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.
51. Ostresh, J.M., WinKle, J.H., Hamashin, V.T., and HouGhten, R. A. (1994b). Peptide libraries: Determination of relative reaction rates of protected amino acids, in competitive couplinGs. Biopolymers 34,1681-1689.
52. Owens, R. A., Gesellchen, P.D., Houchins, B.J., and DiMarchi, R.D. (1991). The rapid identification of HIV protease inhibitors throuGh the synthesis and screeninG of defined peptide mixtures. Biochem. Biophys. Res. Comm. 181,402-408.
53. Pinilla, C, Appel, J.R., Blanc, P., and HouGhten, R. A. (1992). Rapid identification of hiGh affinity peptide liGands usinG positional scanninG synthetic peptide combinatorial libraries. Biotechniques 13,901-905.
54. Pinilla, C., Appel, J.R., and HouGhten, R. A. (1993). Synthetic peptide combinatorial libraries (SPCLs): Identification of the antiGenic determinant of b-endorphin recoGnized by monoclonal antibody 3E7. Gene 128, 71-76.
55. Pinilla, C., Appel, J.R., Blondelle, S. E., Dooley, C.T., Eichler, J., Ostresh, J. M., and HouGhten, R. A. (1994a). Versatility of positional scanninG synthetic combinatorial libraries for the identification of individual compounds. DruG Dev. Res. 33,133-145.
56. Pinilla, C., Appel, J.R., and HouGhten, R.A. (1994b). InvestiGation of antiGen-antibody interactions usinG a soluble nonsupport-bound synthetic decapeptide library composed of four trillion sequences. Biochem. J. 301, 847-853.
57. Pinilla, C., Appel, J., Blondelle, S. E., Dooley, C.T., Dörner, B, Ostresh, J.M., and HouGhten, R.A.(1995). A review of the utility of peptide combinatorial libraries. Biopolymers (Peptide Science) 37,221-240.
58. Scott, J.K., and Smith, G.P. (1990). SearchinG for peptide liGands with an epitope library. Science 249,386-390.
59. Scott, J.K., and CraiG, L. (1994). Random peptide libraries. Curr. Opin. Biotechnol. 5, 40-48.
60. Sham, H.L., Bolis, G., Stein, H.H., FesiK, S.W., Marcotte, P.A., Plattner, J.J., Rempel, C. A., and Greer, J. (1988). Renin inhibitors. DesiGn and synthesis of a new class of conformationally restricted analoGues of anGiotensinoGen. J. Med. Chem. 31, 284-295.
61. Simon, R.J., Kania, R.S., ZucKermann, R.N., Huebner, V.D., Jewell, D. A., Banville, S., NG, S., WanG, L., RosenberG, S., Marlowe, C.K., Spellmeyer, D.C., Tan, R., FranKel, A.D., Santi, D.V., Cohen, F.E., and Bartlett, P.A. (1992). Peptoids: A modular approach to druG discovery. Proc. Natl. Acad. Sci. USA 89, 9367-9371.
62. Smith, G.P., Schultz, D.A., and Ladbury, J.E. (1993). A ribonuclease S-peptide antaGonist discovered with a bacteriophaGe display library. Gene 128,37-42.
63. Tarn, J.P., Heath, W.F., and Merrifield, R.B. (1983). SN2 deprotection of synthetic peptides with a low concentration of HF in dimethyl sulfide: Evidence and application in peptide synthesis. J. Am. Chem. Soc. 105, 6442-6455.
64. Tuchscherer, G., Dörner, B, Sila, U., Kamber, B., and Mutter, M. (1993). The TASP concept: Mimetics of peptide liGands, protein surfaces and foldinG units. Tetrahedron 49, 3559-3575.
65. ZucKermann, R.N. (1993). The chemical synthesis of peptidomimetic libraries. Curr. Opin. Struct. Biol. 3,580-584.
66. ZucKermann, R.N., Martin, E.J., Spellmayer, D.C., Stauber, G. B., ShoemaKer, K.R., Kerr, J.M., FiGliozzi, G.M., Goff, D.A., Siani, M.A., Simon, R.J., Banville, S.C., Brown, E.G., WanG, L., Richter, L.S., and Moos, W.H. (1994). Discovery of nanomolar liGands for 7- transmembrane G-protein-coupled receptors from a diverse N-(substituted) Glycine peptoid library. J. Med. Chem. 37, 2678-2685.