Synthesis of oligopeptide and peptidomimetic libraries

Current Opinion in Chemical Biology

Volumn 1, Issue 1, 1997, Pages 114-119

  Hruby, Victor J ^a   Ahn, Jung Mo ^a   Liao, Subo ^a  

^a University of Arizona ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PEPTIDE; PEPTIDE LIBRARY;

BACTERIOPHAGE; CHEMISTRY; GENETICS; MOLECULAR MIMICRY; REVIEW; SYNTHESIS;

BACTERIOPHAGES; MOLECULAR MIMICRY; PEPTIDE LIBRARY; PEPTIDES;

EID: 0031151963     PISSN: 13675931     EISSN: None     Source Type: Journal    
DOI: 10.1016/s1367-5931(97)80117-2     Document Type: Article

References (60)

1. Geysen MH, Meloen RH, Barteling SJ: Use of peptide synthesis to probe viral antigens for epitopes to a resolution of a single amino acid. Proc Natl Acad Sci USA 1984, 81:3998-4002.
2. Houghten RA: 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 1985, 82:5131-5135.
3. Merrifield RB: Solid phase peptide synthesis. I. The synthesis of a tetrapeptide. J Am Chem Soc 1963, 85:2149-2154.
4. Houghten RA, Pinella C, Blondelle SE, Appel JR, Dooley CT, Guervo JH: Generation and use of synthetic peptide combinatorial libraries for basic research and drug discovery. Nature 1991, 354:84-86.
5. Lam KS, Salmon SE, Hirsch EM, Hruby VJ, Kazmierski WM, Knapp RJ: A new type of synthetic peptide library for identifying ligand-binding activity. Nature 1991, 354:82-84.
6. Hruby VJ: Synthesis of peptide libraries for lead structure screening. In The Practice of Medicinal Chemistry. Edited by Wermuth CA. New York: Academic Press; 1996:135-151.
7. Furka A, Sebestyen F, Asgedom M, Dibo G: General method for rapid synthesis of multicomponent peptide mixture. Int J Peptide Protein Res 1991, 37:487-493.
8. Furka A, Sebestyen F, Asgedom M, Dibo G: Cornucopia of peptides by synthesis. Abstract at the 14th Int Congr Biochem, Prague, Czechoslovakia 1988, Abstract Fr: 013, p 47.
9. Scott JK, Smith GP: Searching for peptide ligands with an epitope library. Science 1990, 249:386-390.
10. Gordon EM, Barrett RW, Dower WJ, Fodor SPA, Gallop MA: Applications of combinatorial technologies to drug discovery. 2. Combinatorial organic synthesis, library screening strategies and future directions. J Med Chem 1994, 37:1385-1401.
11. Rinnova M, Lebl M: Molecular diversity and libraries of structures. Collect Czech Chem Commun 1996, 61:171-231.
12. Thompson LA, Ellman JA: Synthesis and applications of small molecule libraries. Chem Rev 1996, 96:555-600.
13. Hermkens PHH, Ottenheijm HGJ, Rees D: Solid-phase organic reactions: A review of the recent literature. Tetrahedron 1996, 13:4527-4554.
14. Früchtel JS, Jung G: Organic chemistry on solid supports. Angew Chem Int Ed 1996, 35:17-42.
15. Still WC: Discovery of sequence-selective peptide binding by synthetic receptors using encoded combinatorial libraries. Accounts Chem Res 1996, 29:155-163. This issue of Accounts of Chemical Research is devoted to combinatorial chemistry and has several chapters related to various aspects of this field (see also [16], for example).
16. Hsieh-Wilson LC, Xiang XD, Schultz PG: Lessons from the immune system: from catalysts to materials science. Accounts Chem Res 1996, 29:164-170.
17. Terrett NK, Gardner M, Gordon DW, Kobylecki RJ, Steele J: Combinatorial synthesis. The design of compound libraries and their application to drug discovery. Tetrahedron 1995, 30:8135-8173.
18. Baldwin JJ, Henderson I: Recent advances in the generation of small-molecule combinatorial libraries: encoded split synthesis and solid-phase synthetic methodology. Med Res Dev 1996, 16:391-405.
19. Krchnák V, Sepetov NF, Kocis P, Pátek M, Lam KS, Lebl M: Combinatorial libraries of synthetic structures: synthesis, screening, and structure determination. In Combinatorial Libraries: Synthesis, Screening and Application Potential. Edited by Cortese R. Berlin: Walter de Gruyter; 1996:27-52.
20. Spatola AF, Romanovskis P: Cyclic peptide libraries: recent developments. In Combinatorial Peptide and Nonpeptide Libraries. A Handbook. Edited by Jung G. New York: VCH Publishers; 1996:327-347. One of several chapters in an excellent book that covers most aspects of combinatorial chemistry.
21. Lebl M, Pátek M, Kocis P, Krchnak V, Hruby VJ, Salmon SE, Lam KS: Multiple release of equimolar amounts of peptides from a polymeric carrier using orthogonal linkage cleavage chemistry. Int J Peptide Protein Res 1993, 41:201-203.
22. Ivanetich KM, Santi DV: Preparation of equimolar mixtures of peptides by adjustment of activated amino acid concentrations. Methods Enzymol 1996, 267:247-260.
23. Luu T, Pham S, Deshpande S: Automatic multiple peptide synthesis: improvements in obtaining quality peptides. Int J Peptide Protein Res 1996, 47:91-97.
24. Pérez-Payá E, Houghten RA, Blondell SE: Functionalized protein-like structures from conformationally defined synthetic combinatorial libraries. J Biol Chem 1996, 271:4120-4126.
25. McBride JD, Freeman N, Domingo GJ, Leatherbarrow RJ: Selection of chymotrypsin inhibitors from a conformationally-constrained combinatorial peptide library. J Mol Biol 1996, 259:819-827.
26. Songyang Z, Cantley LC: SH2 domain specificity determination using oriented phosphopeptide library. Methods Enzymol 1995, 254:523-535.
27. Han H, Wolfe MM, Brenner S, Janda KD: Liquid-phase combinatorial synthesis. Proc Natl Acad Sci USA 1995, 92:6419-6423. Describes the use of a soluble linear polymer for the synthesis of a peptide library and the development of liquid-phase combinatorial synthesis. The application of a monoclonal antibody against β-endorphin is used as a practical example.
28. Singh J, Ator MA, Jaeger EP, Allen MP, Whipple DA, Soloweij JE, Chowdhary S, Treasurywala AM: Application of genetic algorithms to combinatorial synthesis: a computational approach to lead identification and lead optimization. J Am Chem Soc 1996, 118:1669-1676. A genetic algorithm based strategy is described for the identification or optimization of active leads. The identification of stromelysin substrates from the peptide library is discussed, in support of this method.
29. Sasaki S, Takagi M, Tanaka Y, Maeda M: A new application of a peptide library to identify selective interaction between small peptides in an attempt to develop recognition molecules toward protein surfaces. Tetrahedron Lett 1996, 37:85-88.
30. Shao Y, Still WC: Sequence-selective receptors of peptides. A simple molecular design for construction of large combinatorial libraries of receptors. J Org Chem 1996, 61:6086-6087.
31. Boutin JA, Hennig P, Lambert P-H, Bertin S, Petit L, Mahieu J-P, Serkiz B, Volland J-P, Fauchère AL: Combinatorial peptide libraries: robotic synthesis and analysis by nuclear magnetic resonance, mass spectrometry, tandem mass spectrometry, and high-performance capillary electrophoresis techniques. Anal Biochem 1996, 234:126-141. Many different analytical methods, including 2D NMR spectroscopy and various mass spectrometries, have been used to evaluate synthesized peptide libraries. This article summarizes these methods.
32. Chu Y-H, Kirby DP, Karger BL: Free solution identification of candidate peptides from combinatorial libraries by affinity capillary electrophoresis/mass spectrometry. J Am Chem Soc 1995, 117:5419-5420.
33. Lin M, Shapiro MJ: Mixture analysis in combinatorial chemistry. Application of diffusion-resolved NMR spectroscopy. J Org Chem 1996, 61:7617-7619.
34. Boutin JA, Fauchère AL: Combinatorial peptide synthesis: statistical evaluation of peptide distribution. Trends Pharmacol Sci 1996, 17:8-12. Describes the statistical considerations that are important in the design of a peptide library. This article also shows to what extent one bead-one peptide libraries fulfill these statistical criteria.
35. Lam KS, Wade S, Abdul-Latif F, Lebl M: Application of a dual color detection scheme in the screening of a random combinatorial peptide library. J lmmunol Methods 1995. 180:219-223. A useful way to minimize false positives and other problems in libraries.
36. Buettner JA, Dadd CA, Baumbach GA, Masecar BL, Hammond DJ: Chemically driven peptide libraries: a new resin and methodology for lead identification. Int J Peptide Protein Res 1996, 47:70-83. A new resin for peptide synthesis developed for combinatorial peptide libraries is described as well as the use of the two color analytical technique with this resin.
37. Sioud M, Ferre Ø, Dybwad A: Selection of ligands for polyclonal antibodies from random peptide libraries: potential identification of (auto)antigens that may trigger B and T cell responses in autoimmune diseases. Clin Immunol Immunopathol 1996, 79:105-114.
38. Pasqualini R, Ruoslahti E: Organ targeting in vivo using phage display peptide libraries. Nature 1996, 380:364-366. This paper describes a new approach to studying organ-selective targeting is based on in vivo screening of random peptide libraries. This approach is demonstrated by the identification of peptides capable of mediating selective localization of phage to brain and kidney vessels with significant selectivity over other organs.
39. Mattheakis LC, Dias JM, Dower WJ: Cell-free synthesis of peptide libraries displayed on polysomes. Methods Enzymol 1996, 267:195-207. Describes an approach to random peptide library generation using an in vitro peptide expression system which displays the peptide library on polysomes.
40. Cesareni G, Minenkova O, Donte L, lannolo G, Zucconi A, Citterich MH, Lanfrancotti A, Castagnoli L, Vetriani C: Structural and functional constraints in the display of peptides on filamentous phage capsids. In Combinatorial Libraries: Synthesis, Screening and Application Potential. Edited by Cortese R. Berlin: Walter de Gruyter; 1996:113-126. The structural and functional constraints in the display of random peptide libraries on filamentous phage are concisely discussed.
41. Fisch I, Kontermann RE, Finnern R, Hartley O, Soler-Gonzalez AS, Griffiths AD, Winter G: A strategy of exon shuffling for making large peptide repertoires displayed on filamentous bacteriophage. Proc Natl Acad Sci USA 1996, 93:7761-7766.
42. Malik P, Perham RN: New vectors for peptide display on the surface of filamentous bacteriophage. Gene 1996, 171:49-51.
43. Jacobsson K, Frykberg L: Phage display shot-gun cloning of ligand-binding domains of prokaryotic receptors approaches 100% correct clones. BioTechniques 1996, 20:1070-1081.
44. Nagesha HS, Yu M, Wang L-F: Application of linker-ligation-PCR for construction of phage display epitope libraries. J Virol Meth 1996, 60:147-154.
45. Smith GP, Yu J: In search of dark horses: affinity maturation of phage-displayed ligands. Mol Divers 1996, 2:2-4. Introduces a new strategy for securing all possible clones. In this strategy, clones are selected from the initial library by some criterion of 'fitness,' such as affinity for a particular receptor. The selected clones are then mutagenized to generate a mutant library, which serves as input to the next round of selection.
46. Colas P, Cohen B, Jessen T, Grishina I, McCoy J, Brent R: Genetic selection of peptide aptamers that recognize and inhibit cyclin-dependent kinase 2. Nature 1996, 380:548-550.
47. Wrighton NC, Farrell FX, Chang R, Kashyap AK, Barbone FP, Mulcahy LS, Johnson DL, Barrett RW, Jolliffe LK, Dower WJ: Small peptides as potent mimetics of the protein hormone erythropoietin. Science 1996, 273:458-463. A good example of the application of a random phage display library and affinity selection methods to identify small peptide ligands. Here a small 14-residue cyclic peptide mimic of erythropoietin has been isolated which shares no sequence or structural homology to erythropoietin (EPO), but binds to and activates the EPO receptor.
48. Schumacher TNM, Mayr LM, Minor DL Jr, Milhollen MA, Burgess MW, Kim PS: Identification of D-peptide ligands through mirror-image phage display. Science 1996, 271:1854-1857. This new strategy led to the successful identification of cyclic D-peptide ligands for the Src homology 3 domain of c-Src. In this approach, a D-protein was synthesized to select peptide ligands from a random L-amino-acid phage display library. For reasons of symmetry, the mirror images of these phage-displayed peptides interact with the target protein of the natural handedness.
49. Yanofsky SD, Baldwin DN, Butler JH, Holden FR, Jacobs JW, Balasubramanian P, Chinn JP, Cwirla SE, Peters-Bhatt E, Whitehorn EA et al.: High affinity type I interleukin I receptor antagonists discovered by screening recombinant peptide libraries. Proc Natl Acad Sci USA 1996, 93:7381-7386.
50. Yamanaka HI, Inoue T, Ikeda-Tanaka O: Chicken monoclonal antibody isolated by a phage display system. J Immunol 1996, 157:1156-1162.
51. Houston ME Jr, Wallace A, Bianchi E, Pessi A, Hodges RS: Use of a conformationally restricted secondary structural element to display peptide libraries: a two-stranded α-helical coiled-coil stabilized by lactam bridges. J Mol Biol 1996, 262:270-282.
52. Jiráček J, Yiotakis A, Vincent B, Checler F, Dive V: Development of the first potent and selective inhibitor of the zinc endopeptidase neurolysin using a systematic approach based on combinatorial chemistry of phosphinic peptides. J Biol Chem 1996, 271:19606-19611.
53. Müller K, Gombert FO, Manning U, Grossmüller F, Graff P, Zaegel H, Zuber JF, Freuler F, Tschopp C, Baumann G: Rapid identification of phosphopeptide ligands for SH2 domains. J Biol Chem 1996, 271:16500-16505. This paper describes a method for the identification of high-affinity ligands to SH2 domains by fluorescence-activated bead sorting.
54. Dörner B, Husar GM, Ostresh JM, Houghton RA: The synthesis of peptidomimetic combinatorial libraries through successive amide alkylations. Bioorg Med Chem 1996, 4:709-715.
55. Rockwell A, Melden M, Copeland RA, Decicco CP, Degrado WF: Complementarity of combinatorial chemistry and structure-based ligand design: application to the discovery of novel inhibitors of matrix metalloproteinases. J Am Chem Soc 1996, 118:10337-10338.
56. Cheng Y, Suenaga T, Still WC: Sequence-selective peptide binding with a peptido-A,B-trans-steroidal receptor selected from an encoded combinatorial receptor library. J Am Chem Soc 1996, 118:1813-1814.
57. Tempest PA, Brown SD Armstrong RW: Solid-phase, parallel syntheses by Ugi multicomponent condensation. Angew Chem Int Ed 1996, 35:640-642. This novel approach has all the advantages of solid-phase synthesis, and at the same time, the diversity of the libraries is controlled by the number of components and their availability.
58. Hruby VJ, Shenderovich M, Lam K, Lebl M: Design considerations and computer modeling related to the development of molecular scaffolds and peptide mimetics for combinatorial chemistry. Mol Divers 1996, 2:46-56. This paper describes the use of computational chemistry to evaluate topographical similarities and differences of scaffolds and mimetics.
59. Boger DL, Tarby CM, Myers PL, Caporale LH: Generalized dipeptidomimetic template: solution phase parallel synthesis of combinatorial libraries. J Am Chem Soc 1996, 118:2109-2110.
60. Cheng S, Comer DC, Williams JP, Myers PL, Boger DL: Novel solution phase strategy for the synthesis of chemical libraries containing small organic molecules. J Am Chem Soc 1996, 118:2567-2573.