The combinatorial library: A multifunctional resource

Biotechnology Progress

Volumn 12, Issue 6, 1996, Pages 729-743

  Schultz, Jane S ^a   Schultz, Jerome S ^a  

^a UNIVERSITY OF PITTSBURGH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOSYNTHESIS; BIOTECHNOLOGY; DRUG PRODUCTS; ENZYMES;

BINDING AGENTS; COMBINATORIAL LIBRARIES; MULTIFUNCTIONAL RESOURCE; PARALLEL SYNTHESIS; PEPTIDES;

PROTEINS;

ANTIBODY; PEPTIDE; PEPTIDE LIBRARY;

AMINO ACID SEQUENCE; BIOTECHNOLOGY; CHEMISTRY; GENE LIBRARY; METHODOLOGY; PEPTIDE SYNTHESIS; REVIEW; SYNTHESIS;

AMINO ACID SEQUENCE; ANTIBODIES; BIOTECHNOLOGY; GENE LIBRARY; PEPTIDE BIOSYNTHESIS; PEPTIDE LIBRARY; PEPTIDES;

EID: 0030292770     PISSN: 87567938     EISSN: None     Source Type: Journal    
DOI: 10.1021/bp960081w     Document Type: Review

References (66)

1. Bartel, D. P.; Szostak, J. W. Isolation of New Ribozymes from a Large Pool of Random Sequences. Science 1993, 261, 1411-1418.
2. Baumbach, G. A.; Hammond, D. J. Protein Purification Using Affinity Ligands Deduced from Peptide Libraries. BioPharm 1992 (May), 24-35.
3. Bock L. C.; Griffin, L. C.; Latham, J. A.; Vermaas, E. H.; Toole, J. J. Selection of Single-Stranded DNA Molecules That Bind and Inhibit Human Thrombin. Nature 1992, 355, 564-566.
4. Borman, S. Combinatorial chemists focus on small molecules, molecular recognition, and automation. Chem. Eng. News 1996, Feb. 12, 29.
5. Boublik, Y.; DiBonito, P.; Jones, I. Eukaryotic Virus Display: Engineering the Major Surface Glycoporteins of the Autographa California Nuclear Polyhedrosis Virus (ACNPV) for the Presentation of Foreign Proteins on the Virus Surface. Bio / Technology 1995, 13, 1079-1084.
6. Brenner, S.; Lerner, R. A. Encoded Combinatorial Chemistry. Proc. Natl. Acad. Sci. U.S.A. 1992, 89, 5381-5383.
7. Caflisch, A.; Karplus, M. Computational Combinatorial Chemistry for De Novo Ligand Design: Review and Assessment. Perspect. Drug Discovery Des. 1995, 3, 51-84.
8. Cheng, Y.; Suenaga, T.; Still, W. C. Sequence-Selective Peptide Binding with a Peptido-A,B-trans-steroidal Receptor Selected from an Encoded Combinatorial Library. J. Am. Chem. Soc. 1996, 118, 1813-1814.
9. Chu, Y.-H.; Avila, L.; Biebuyck, H.; Whitesides, G. Affinity Capillary Electrophoresis to Identify the Peptide in A Peptide Library That Binds Most Tightly to Vancomycin. J. Org. Chem. 1993, 58, 648-652.
10. Clackson, T.; Hoogenboom, H. R.; Griffiths, A. D.; Winter, G. Making Antibody Fragments Using Phage Display Libraries. Nature 1991, 352, 624-628.
11. Combs, A.; Kapoor, T.; Feng, S.; Chen, J.; Daude-Snow, L.; Schreiber, S. J. Protein Structure-Based Combinatorial Chemistry: Discovery of Non-Peptide Binding Elements to Src SH3 Domain. J. Am. Chem. Soc. 1996, 118, 287-288.
12. Cwirla, S. E.; Peters, E. A.; Barrett, R. W.; Dower, R. Peptides On Phage: A Vast Library of Peptides for Identifying Ligands. Proc. Natl. Acad. Sci. U.S.A. 1990, 87, 6378-6382.
13. Ecker, D. J.; Crooke, S. T. Combinatorial Drug Discovery: Which Method will Produce the Greatest Value? Bio / Technology 1995, 13, 351-360.
14. Ellington, A. D.; Szotak, J. W. In Vitro Selection of RNA Molecules That Bind Specific Ligands. Nature 1990, 346, 818-822.
15. Ellman, J. A. Variants of Benzodiazepines. J. Am. Chem. Soc. 1992, 114, 10997.
16. Erickson, B. W.; Merrifield, R. B. In The Proteins; Neurath, H., Hill, R. L., Eds.; Academic: New York, 1976; pp 255-257.
17. Felici, T.; Castagnoli, L.; Musaccchio, A.; Jappelli, R.; Cesareni, G. J. Mol. Biol. 1991, 222, 301-310.
18. Fodor, S. P.; Read, J. L.; Pirrung, M. C.; Stryer, L.; Lu, A. T.; Solas, D. Light-Directed, Spatially Addressable Parallel Chemical Synthesis. Science 1991, 251, 767-773.
19. Francisco, J.; Earhart, C.; Georgiou, G. Transport and Anchoring of Beta-Lactamase to the External Surface of E. Coli. Proc. Natl. Acad. Sci. U.S.A. 1992, 89, 2713-2717.
20. Georgiou, G.; Poetschke, H.; Stathopoulos, C.; Francisco, J. Practical Applications of Engineering Gram-Negative Bacterial Cell Surfaces. TIBTECH 1993, 11, 6-10.
21. Geysen, H. M.; Meloen, R. N.; Barleling, S. J. Use of peptide synthesis to probe viral antigens for epitopes to a resolution of a single amino acid. Proc. Natl. Acad. Sci. U.S.A. 1984, 81, 3998-4002.
22. Glaser, S. M.; Yelton, D. E.; Huse, W. D. Antibody Engineering By Condon-Based Mutagenesis in a Filamentous Phage Vector System. J. Immunol. 1992, 149, 3903-3913.
23. Goud, G. N.; Patwardhan, A. V.; Beckman, E. C.; Ataai, M. M.; Koepsel, R. R. Selection of a Specific Peptide Ligand for Immobilized Metals Using a Phage Display Library: Application to Protein Separation Using IMAC. Int. J. Bio-Chromatogr., in press.
24. Gram, H.; Marconi, L. A.; Barbas, C. F.; Collet, T. A; Lerneo, R. A.; Kang, A. S. In vitro selection and affinity maturation of antibodies from a naive combinatorial immunoglobulin library. Proc. Natl. Acad. Sci. 1992, 89, 3576-3580.
25. Han, H.; Wolfe, M. M.; Brenner, S.; Janda, K. D. Liquid-Phase Combinatorial Synthesis. Proc. Natl. Acad. Sci. U.S.A. 1995, 92, 6419-6423.
26. Hoogenboom, H. R.; Griffith, A. D.; Johnson, K. S.; Chiswell, D. J.; Hudson, P.; Winter, G. Multi-Subunit Proteins on the Surface of Filamentous Phage: Methodologies for Displaying Antibody (Fab) Heavy and Light Chains. Nucleic Acids Res. 1991,19, 4133-4137.
27. 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. U.S.A. 1985, 82, 5131-5135.
28. Houghten, R. A.; Dooley, C. T. The Use of Synthetic Peptide Combinatorial Libraries for the Determination of Peptide Ligands in Radio-Receptor Assays-Opioid-Peptides. Bioorg. Med. Chem. Lett. 1993, 3, 405-412.
29. Houghten, R. A.; Pinilla, C.; Blondelle, S. E.; Appel, J. R.; Dooley, C. T.; Cuervo, J. H. Generation and Use of Synthetic Peptide Combinatorial Libraries for Basic Research and Drug Discovery. Nature 1991, 354, 84-86.
30. Huang, X.; Boxer, S. G. Discovery of New Ligand Binding Pathways in Myoglobin by Random Mutagenesis Nature Struct. Biol. 1994, 1, 226-229.
31. Huse, W. D.; Sastry, L.; Iverson, S. A.; Kang, A. S.; Alting-Mees, M.; Burton, D. R.; Benkovic, S. J.; Lerner, R. A. Generation of A Large Combinatorial Library of the Immunoglobulin Repertoire In Phage Lambda. Science 1989, 246, 1275-1281.
32. Janda, K. D. New Strategies for the Design of Catalytic Antibodies. Biotechnol. Prog. 1990, 6, 178-181.
33. Jung, G.; Beck-Sickinger, A. Multiple Peptide Synthesis Methods and Their Applications. Angew. Chem., Int. Ed. Engl. 1992, 31, 367-486.
34. Kang, A. S.; Barbas, C. F., III; Janda, K. D.; Benkovic, S.; Lerner, R. A. Linkage of Recognition and Replication Functions By Assembling Combinatorial Antibody Fab Libraries Along Phage Surfaces. Proc. Natl. Acad. Sci. U.S.A. 1991a, 88, 4363-4366.
35. Rang, A. S.; Jones, T. M.; Burton, D. R. Antibody Redesign By Chain Shuffling from Random Combinatorial Immunoglobulin Libraries. Proc. Natl. Acad. Sci. U.S.A. 1991b, 88, 11120-11123.
36. Kay, B. K.; Adey, N. B.; He, Y. S.; Manfredi, J. P.; Mataragnon, A. H.; Fowlkes, D. M. An M13 Phage Library Displaying Random 38-Amino-Acid-Peptides as a Sosurce of Novel Sequences with Affinity to Selected Targets Genes. Gene 1993, 128, 59-65.
37. Lam, K. S.; Salmon, S. E.; Hersh, E. M.; Hruby, V. J.; Kazmierski, W. M.; Knapp, R. J. A new type of synthetic peptide library for identifying ligand-binding activity. Nature 1991, 354, 82-84 (published errata appear in Nature 1992, 358, 434 and Nature 1992, 360, 768).
38. Lebl, M.; Krehnak, V.; Sseptetov, N.; Seligmann, B.; Strop, P.; Felder, S.; Lam, R. One Bead One Structure Combinatorial Libraries. Biopolymers (Pept. Sci.) 1995, 37, 177-198.
39. Lerner, R. A.; Rang, A. D.; Bain, J. D.; Burton, D. R.; Barbas, C. F., III. Antibodies without Immunization. Science 1992, 258, 1313-1314.
40. Li, B.; Tom, J. Y. R.; Oare, D.; Yen, R.; Fairbrother, W. J.; Wells, J. A.; Cunningham, B. C. Minimization of a Polypeptide Hormone. Science 1995, 270, 1657-1660.
41. Light, J.; Lerner, R. A. Display of Dimeric Bacterial Alkaline Phosphatase on the Major Coat Protein of Filamentous Baceriophage. Bioorg. Med. Chem. Lett. 1992, 3, 1073-1079.
42. Little, M.; Fuchs, P.; Breitling, F.; Dubel, S. Bacterial Surface Presentation of Proteins and Peptides: An Alternative to Phage Technology? Trends Biotechnol. 1993, 11, 3-5.
43. Marks, J.; Hoogenboom, H.; et al. By-Passing Immunization. Human Antibodies from V-Gene Libraries Displayed on Phage. J. Mol. Biol. 1991, 222, 581-597.
44. Matthews, D.; Wells, J. A. Substrate Phage: Selection of Protease Substrates by Monovalent Phage Display. Science 1993, 260, 1113-1117.
45. McCafferty, J.; Jackson, R. H.; Chiswell, D. J. Phage Enzymes: Expression and Affinity Chromatography of Functional Alkaline Phosphatase on the Surface of Bacteriophage. Protein Eng. 1991, 4, 955-961.
46. Menger, F. M.; Eliseev, A. V.; Migulin, V. A. Phosphatase Catalysis Developed Via Combinatorial Organic Chemistry. J. Org. Chem. 1995, 60, 6666-6667.
47. Nicolaou, K. C.; Xiao, X.-Y.; Parandoosh, Z.; Senyei, A.; Nova, M. Angew. Chem., Int. Ed. Engl. 1995, 34, 2289-2291.
48. Oldenburg, K. R.; Loganathan, D.; Goldstein, I. J.; Schultz, P. G.; Gallop, M. A. Peptide Ligands for A Sugar-Binding Protein Isolated from A Random Peptide Library. Proc. Natl. Acad. Sci. U.S.A. 1992, 89, 5393-5397.
49. Parmley S. F.; Smith G. P. Antibody-Selectable Filamentous fd Phage Vectors: Affinity Purification of Target Genes. Genes 1988, 73, 305-318.
50. Pinilla, C.; Appel, J. R.; Houghten, R. A. Synthetic Peptide Combinatorial Libraries (SPCLS)-Identification of the Antigenic Determinant of Beta-Endorphin Recognized by Monoclonal Antibody-3E7. Gene 1993, 128, 71-76.
51. Pinilla, C.; Appel, J.; Dooley, C.; Dorner, B.; Eichler, J.; Ostresh, J.; Houghton, R. A Review of the Utility of Soluble Combinatorial Libraries. Biopolymers 1995, 37, 221-240.
52. Pistor, S.; Hoborn, G. Expression of Viral Hemegglutinan On the Surface of E. Coli. Klin. Wochenschr. 1989, 66, 110-116.
53. Pollack, S.; Jacobs, J.; Schultz, P. Selective Chemical Catalysis by an Antibody. Science 1986, 234, 1570-1572.
54. Rigler, R. Fluorescence Correlations, Single Molecule Detection and Large Number Screening: Applications in Biotechnology. J. Biotechnol. 1995, 41, 177-186.
55. Sarvetnick, N.; Gurushanthaiah, D.; Han, N.; Prudent, J.; Schultz, P.; Lerner, R. Increasing the Chemical Potential of the Germ-Line Antibody Repertoire. Proc. Natl. Acad. Sci. U.S.A. 1993, 90, 4008-4011.
56. Sastry, L.; Alting-Mees, M.; Huse, W. D.; Short, J. M.; Sorge, J. A.; Hay, B. N.; Janda, K. D.; Benkovic, S. J.; Lerner, R. A. Cloning of the Immunological Repertoire in Escherichia Coli for Generation of Monoclonal Catalytic Antibodies: Construction of a Heavy Chain Variable Region-Specific cDNA Library. Proc. Natl. Acad. Sci. U.S.A. 1989, 86, 5728-5732.
57. Scott, J. K.; Smith, G. P. Searching for Peptide Ligands with an Epitope Library. Science 1990, 249, 386-390.
58. Sears, P.; Wang, C.-H. Engineering Enzymes for Bioorganic Synthesis: Peptide Bond Formation. Biotechnol. Prog. 1996, 12, 423-433.
59. Simon, R. J.; Kania, R. S.; Zuckermann, R. N.; Huebner, V. D.; Jewell, D. A.; Banville, S.; Ng, S.; Wang, L.; Rosenberg, S.; Marlow, C. K.; et al. Peptoids: A Modular Approach to Drug Discovery. Proc. Natl. Acad. Sci. U.S.A. 1992, 89, 9367-9371.
60. Still, W. C. Discovery of Sequence-Selective Peptide Binding by Synthetic Receptors Using Encoded Combinatorial Libraries. Acc. Chem. Res. 1996, 29, 155-163.
61. Thompson, L.; Ellman, J. Synthesis and Applications of Small Molecule Libraries. Chem. Rev. 1996, 96, 555-600.
62. Tramontano, A.; Janda, K.; Lerner, R. Catalytic Antibodies. Science 1986, 234, 1566-1570.
63. Wrighton, N.; Farrell, F.; Chang, R.; Kashyap, A. K.; Barbone, F. P.; Mulcahy, L. S.; Johnson, D. L.; Barrett, R. W.; Jolliffe, L. K.; Dover, W. J. Small Peptides as Potent Mimetics of the Protein Hormone Erythropoietin. Science 1996, 273, 458-464.
64. York, J. D.; Li, P.; Gardell, S. J. Combinatorial mutagenesis of the reactive site region in plasminogen activator inhibitor I. J. Biol. Chem. 1991, 266, 8595-8500.
65. Zebedee, S. L.; Barbas, C. F.; Hom, Y. L.; Caothien, R. H.; Graff, R.; DeGraw, J.; Pyati, J.; LaPolla, R.; Burton, D. R.; Lerner, R. A.; et al. Human Combinatorial Antibody Libraries to Hepatitis B Surface Antigen. Proc. Natl. Acad. Sci. U.S.A. 1992, 89, 3175-3179.
66. Zuckerman, R. N.; Kerr, J. M.; Siani, M. A.; Banville, S. C.; Santi, D. V. Identification of Highest-Affinity Ligands by Affinity Selection from Equimolar Peptide Mistures Generated by Robotic Synthesis. Proc. Natl. Acad. Sci. U.S.A. 1992, 89, 4505-4509.