Peptoid Ligands That Bind Selectively to Phosphoproteins

Overview

Journal Bioorg Med Chem Lett

Specialty Biochemistry

Date 2011 Jul 12

PMID 21742492

Citations 12

Authors

Di Cai

A-Young Lee

Cheng-Ming Chiang

Thomas Kodadek

Affiliations

Soon will be listed here.

Abstract

Synthetic equivalents of phosphoprotein-specific antibodies would be valuable reagents for biological research, since these antibodies can often be difficult to produce. Protein phosphorylation is thought to result in significant conformational changes in most substrate proteins. Therefore, one approach might be to simply screen combinatorial libraries for ligands to the phosphorylated state in the hope of isolating a ligand that binds to a pocket created by the conformational shift. In this study, we probe this strategy by screening a peptoid library for ligands to the phosphorylated form of the Brd4 chromatin adaptor and transcriptional coactivator protein. We find that peptoids with high selectivity for binding to the phosphorylation form of Brd4 can indeed be isolated in this screen. Moreover, these ligands do not bind promiscuously to other phospho-proteins. However, attempts to employ these reagents as antibody substitutes in an immunoaffinity purification-like application showed that they do not perform as well as bona fide antibodies and that significant optimization will be required. This study highlights the potential and current limitations of a naïve library screening strategy for phosphoprotein-specific antibody surrogates.

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References

Wu S, Thomas M, Hou S, LIKHITE V, Chiang C . Isolation of mouse TFIID and functional characterization of TBP and TFIID in mediating estrogen receptor and chromatin transcription. J Biol Chem. 1999; 274(33):23480-90. DOI: 10.1074/jbc.274.33.23480. View

Li W, Heinze J, Haehnel W . Site-specific binding of quinones to proteins through thiol addition and addition-elimination reactions. J Am Chem Soc. 2005; 127(17):6140-1. DOI: 10.1021/ja050974x. View

Simpson L, Burdine L, Dutta A, Feranchak A, Kodadek T . Selective toxin sequestrants for the treatment of bacterial infections. J Am Chem Soc. 2009; 131(16):5760-2. PMC: 2810561. DOI: 10.1021/ja900852k. View

Heffetz D, Fridkin M, Zick Y . Antibodies directed against phosphothreonine residues as potent tools for studying protein phosphorylation. Eur J Biochem. 1989; 182(2):343-8. DOI: 10.1111/j.1432-1033.1989.tb14836.x. View

Alluri P, Liu B, Yu P, Xiao X, Kodadek T . Isolation and characterization of coactivator-binding peptoids from a combinatorial library. Mol Biosyst. 2007; 2(11):568-79. DOI: 10.1039/b608924k. View

Chiang C, Ge H, Wang Z, Hoffmann A, Roeder R . Unique TATA-binding protein-containing complexes and cofactors involved in transcription by RNA polymerases II and III. EMBO J. 1993; 12(7):2749-62. PMC: 413525. DOI: 10.1002/j.1460-2075.1993.tb05936.x. View

Ranjitkar P, Brock A, Maly D . Affinity reagents that target a specific inactive form of protein kinases. Chem Biol. 2010; 17(2):195-206. PMC: 2871157. DOI: 10.1016/j.chembiol.2010.01.008. View

Filippakopoulos P, Qi J, Picaud S, Shen Y, Smith W, Fedorov O . Selective inhibition of BET bromodomains. Nature. 2010; 468(7327):1067-73. PMC: 3010259. DOI: 10.1038/nature09504. View

Olivos H, Alluri P, Reddy M, Salony D, Kodadek T . Microwave-assisted solid-phase synthesis of peptoids. Org Lett. 2002; 4(23):4057-9. DOI: 10.1021/ol0267578. View

10.

Simon R, Kania R, Zuckermann R, Huebner V, Jewell D, Banville S . Peptoids: a modular approach to drug discovery. Proc Natl Acad Sci U S A. 1992; 89(20):9367-71. PMC: 50132. DOI: 10.1073/pnas.89.20.9367. View

11.

Wu S, Chiang C . The double bromodomain-containing chromatin adaptor Brd4 and transcriptional regulation. J Biol Chem. 2007; 282(18):13141-5. DOI: 10.1074/jbc.R700001200. View

12.

Czernik A, Girault J, Nairn A, Chen J, Snyder G, Kebabian J . Production of phosphorylation state-specific antibodies. Methods Enzymol. 1991; 201:264-83. DOI: 10.1016/0076-6879(91)01025-w. View

13.

Alluri P, Reddy M, Bachhawat-Sikder K, Olivos H, Kodadek T . Isolation of protein ligands from large peptoid libraries. J Am Chem Soc. 2003; 125(46):13995-4004. DOI: 10.1021/ja036417x. View

14.

Xiao X, Yu P, Lim H, Sikder D, Kodadek T . A cell-permeable synthetic transcription factor mimic. Angew Chem Int Ed Engl. 2007; 46(16):2865-8. DOI: 10.1002/anie.200604485. View

15.

Liu B, Burdine L, Kodadek T . Chemistry of periodate-mediated cross-linking of 3,4-dihydroxylphenylalanine-containing molecules to proteins. J Am Chem Soc. 2006; 128(47):15228-35. PMC: 2568988. DOI: 10.1021/ja065794h. View

16.

Paradela A, Albar J . Advances in the analysis of protein phosphorylation. J Proteome Res. 2008; 7(5):1809-18. DOI: 10.1021/pr7006544. View

17.

Burdine L, Gillette T, Lin H, Kodadek T . Periodate-triggered cross-linking of DOPA-containing peptide-protein complexes. J Am Chem Soc. 2004; 126(37):11442-3. DOI: 10.1021/ja045982c. View

18.

Lim H, Archer C, Kodadek T . Identification of a peptoid inhibitor of the proteasome 19S regulatory particle. J Am Chem Soc. 2007; 129(25):7750-1. PMC: 2543931. DOI: 10.1021/ja072027p. View

19.

Chiang C, Roeder R . Expression and purification of general transcription factors by FLAG epitope-tagging and peptide elution. Pept Res. 1993; 6(2):62-4. View

20.

Gomika Udugamasooriya D, Dineen S, Brekken R, Kodadek T . A peptoid "antibody surrogate" that antagonizes VEGF receptor 2 activity. J Am Chem Soc. 2008; 130(17):5744-52. DOI: 10.1021/ja711193x. View