Enzyme-mediated Spatial Segregation on Individual Polymeric Support Beads: Application to Generation and Screening of Encoded Combinatorial Libraries

Overview

Journal Proc Natl Acad Sci U S A

Specialty Science

Date 1996 Aug 6

PMID 8710846

Citations 7

Authors

J Vagner

G Barany

K S Lam

V Krchnak

N F Sepetov

J A Ostrem

P Strop

M Lebl

Affiliations

Soon will be listed here.

Abstract

Proteolysis of short N alpha-protected peptide substrates bound to polyoxyethylene-polystyrene beads releases selectively free amino sites in the enzyme-accessible "surface" area. The substantial majority of functional sites in the "interior" of the polymeric support are not reached by the enzyme and remain uncleaved (protected). Subsequent synthesis with two classes of orthogonal protecting groups-N alpha-tert-butyloxycarbonyl (Boc) and N alpha-9-fluorenylmethyloxy-carbonyl (Fmoc)-allows generation of two structures on the same bead. The surface structure is available for receptor interactions, whereas the corresponding interior structure is used for coding. Coding structures are usually readily sequenceable peptides. This "shaving" methodology was illustrated by the preparation of a peptide-encoded model peptide combinatorial library containing 1.0 x 10(5) members at approximately 6-fold degeneracy. From this single library, good ligands were selected for three different receptors: anti-beta-endorphin anti-body, streptavidin, and thrombin, and the binding structures were deduced correctly by sequencing the coding peptides present on the same beads.

Citing Articles

Reflections on a Copenhagen-Minneapolis Axis in Bioorganic Chemistry.

Barany G, Hansen P Molecules. 2024; 29(6).

PMID: 38542953 PMC: 10974982. DOI: 10.3390/molecules29061317.

Abiotic peptides as carriers of information for the encoding of small-molecule library synthesis.

Rossler S, Grob N, Buchwald S, Pentelute B Science. 2023; 379(6635):939-945.

PMID: 36862767 PMC: 10064805. DOI: 10.1126/science.adf1354.

Xenoprotein engineering via synthetic libraries.

Gates Z, Vinogradov A, Quartararo A, Bandyopadhyay A, Choo Z, Evans E Proc Natl Acad Sci U S A. 2018; 115(23):E5298-E5306.

PMID: 29784819 PMC: 6003312. DOI: 10.1073/pnas.1722633115.

Synthesis and characterization of dual-functionalized core-shell fluorescent microspheres for bioconjugation and cellular delivery.

Behrendt J, Nagel D, Chundoo E, Alexander L, Dupin D, Hine A PLoS One. 2013; 8(3):e50713.

PMID: 23526923 PMC: 3602537. DOI: 10.1371/journal.pone.0050713.

Real-Time Imaging of Protease Action on Substrates Covalently Immobilised to Polymer Supports.

Deere J, McConnell G, Lalaouni A, Maltman B, Flitsch S, Halling P Adv Synth Catal. 2009; 349(8-9):1321-1326.

PMID: 19779571 PMC: 2749704. DOI: 10.1002/adsc.200700044.

References

Sachdev G, Fruton J . Secondary enzyme-substrate interactions and the specificity of pepsin. Biochemistry. 1970; 9(23):4465-70. DOI: 10.1021/bi00825a001. View

Krchnak V, Weichsel A, Cabel D, Lebl M . Linear presentation of variable side-chain spacing in a highly diverse combinatorial library. Pept Res. 1995; 8(4):198-205. View

Geysen H, Rodda S, Mason T . A priori delineation of a peptide which mimics a discontinuous antigenic determinant. Mol Immunol. 1986; 23(7):709-15. DOI: 10.1016/0161-5890(86)90081-7. View

Fodor S, Read J, Pirrung M, Stryer L, Lu A, Solas D . Light-directed, spatially addressable parallel chemical synthesis. Science. 1991; 251(4995):767-73. DOI: 10.1126/science.1990438. View

Furka A, Sebestyen F, Asgedom M, Dibo G . General method for rapid synthesis of multicomponent peptide mixtures. Int J Pept Protein Res. 1991; 37(6):487-93. DOI: 10.1111/j.1399-3011.1991.tb00765.x. View

Lam K, Salmon S, Hersh E, Hruby V, Kazmierski W, Knapp R . A new type of synthetic peptide library for identifying ligand-binding activity. Nature. 1991; 354(6348):82-4. DOI: 10.1038/354082a0. View

Houghten R, Pinilla C, Blondelle S, Appel J, Dooley C, Cuervo J . Generation and use of synthetic peptide combinatorial libraries for basic research and drug discovery. Nature. 1991; 354(6348):84-6. DOI: 10.1038/354084a0. View

Krchnak V, Vagner J . Color-monitored solid-phase multiple peptide synthesis under low-pressure continuous-flow conditions. Pept Res. 1990; 3(4):182-93. View

Kelly A, Maraganore J, Bourdon P, Hanson S, Harker L . Antithrombotic effects of synthetic peptides targeting various functional domains of thrombin. Proc Natl Acad Sci U S A. 1992; 89(13):6040-4. PMC: 49433. DOI: 10.1073/pnas.89.13.6040. View

10.

Nikolaiev V, Stierandova A, Krchnak V, Seligmann B, Lam K, Salmon S . Peptide-encoding for structure determination of nonsequenceable polymers within libraries synthesized and tested on solid-phase supports. Pept Res. 1993; 6(3):161-70. View

11.

DEWITT S, Kiely J, Stankovic C, Schroeder M, Cody D, Pavia M . "Diversomers": an approach to nonpeptide, nonoligomeric chemical diversity. Proc Natl Acad Sci U S A. 1993; 90(15):6909-13. PMC: 47044. DOI: 10.1073/pnas.90.15.6909. View

12.

Needels M, Jones D, Tate E, Heinkel G, Kochersperger L, Dower W . Generation and screening of an oligonucleotide-encoded synthetic peptide library. Proc Natl Acad Sci U S A. 1993; 90(22):10700-4. PMC: 47845. DOI: 10.1073/pnas.90.22.10700. View

13.

Ohlmeyer M, SWANSON R, Dillard L, Reader J, Asouline G, Kobayashi R . Complex synthetic chemical libraries indexed with molecular tags. Proc Natl Acad Sci U S A. 1993; 90(23):10922-6. PMC: 47893. DOI: 10.1073/pnas.90.23.10922. View

14.

Gallop M, Barrett R, Dower W, Fodor S, Gordon E . Applications of combinatorial technologies to drug discovery. 1. Background and peptide combinatorial libraries. J Med Chem. 1994; 37(9):1233-51. DOI: 10.1021/jm00035a001. View

15.

Gordon E, Barrett R, Dower W, Fodor S, Gallop M . Applications of combinatorial technologies to drug discovery. 2. Combinatorial organic synthesis, library screening strategies, and future directions. J Med Chem. 1994; 37(10):1385-401. DOI: 10.1021/jm00036a001. View

16.

Lebl M, Krchnak V, Sepetov N, Seligmann B, Strop P, Felder S . One-bead-one-structure combinatorial libraries. Biopolymers. 1995; 37(3):177-98. DOI: 10.1002/bip.360370303. View

17.

Kasafirek E, Fric P, Slaby J, Malis F . p-Nitroanilides of 3-carboxypropionyl-peptides. Their cleavage by elastase, trypsin, and chymotrypsin. Eur J Biochem. 1976; 69(1):1-13. DOI: 10.1111/j.1432-1033.1976.tb10852.x. View