Targeting diverse protein-protein interaction interfaces with α/β-peptides derived from the Z-domain scaffold

Proceedings of the National Academy of Sciences of the United States of America

Volumn 112, Issue 15, 2015, Pages 4552-4557

  Checco, James W ^a   Kreitler, Dale F ^a   Thomas, Nicole C ^a   Belair, David G ^b   Rettko, Nicholas J ^a   Murphy, William L ^b,c   Forest, Katrina T ^a   Gellman, Samuel H ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

^b University of Wisconsin Madison   (United States)

^c UNIVERSITY OF WISCONSIN SCHOOL OF MEDICINE AND PUBLIC HEALTH   (United States)

Author keywords

Foldamers; Inhibitors; Molecular recognition; Protein protein interactions; peptides

Indexed keywords

ALPHA AMINO ACID; BETA AMINO ACID; IMMUNOGLOBULIN G; IMMUNOGLOBULIN G1; IMMUNOGLOBULIN G2; MOLECULAR SCAFFOLD; OLIGOMER; TUMOR NECROSIS FACTOR ALPHA; VASCULOTROPIN; VASCULOTROPIN 165; VASCULOTROPIN C; PEPTIDE; PROTEIN; PROTEIN BINDING; VASCULOTROPIN A; VEGFA PROTEIN, HUMAN;

AMINO ACID SUBSTITUTION; ANGIOGENESIS; ARTICLE; CIRCULAR DICHROISM; COMPLEX FORMATION; CONTROLLED STUDY; CRYSTAL STRUCTURE; DISSOCIATION CONSTANT; DISULFIDE BOND; ENZYME LINKED IMMUNOSORBENT ASSAY; FLUORESCENCE POLARIZATION; HUMAN; HUMAN CELL; HYDROGEN BOND; PHAGE DISPLAY; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DEGRADATION; PROTEIN DOMAIN; PROTEIN PROTEIN INTERACTION; PROTEIN SECONDARY STRUCTURE; RECEPTOR BINDING; UMBILICAL VEIN ENDOTHELIAL CELL; AMINO ACID SEQUENCE; BINDING SITE; CELL CULTURE; CELL PROLIFERATION; CELL SURVIVAL; CHEMICAL STRUCTURE; CHEMISTRY; CYTOLOGY; DOSE RESPONSE; DRUG EFFECTS; GENETICS; METABOLISM; MOLECULAR GENETICS; PROTEIN TERTIARY STRUCTURE; SEQUENCE HOMOLOGY; X RAY CRYSTALLOGRAPHY;

AMINO ACID SEQUENCE; BINDING SITES; CELL PROLIFERATION; CELL SURVIVAL; CELLS, CULTURED; CRYSTALLOGRAPHY, X-RAY; DOSE-RESPONSE RELATIONSHIP, DRUG; HUMAN UMBILICAL VEIN ENDOTHELIAL CELLS; HUMANS; IMMUNOGLOBULIN G; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PEPTIDES; PROTEIN BINDING; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID; TUMOR NECROSIS FACTOR-ALPHA; VASCULAR ENDOTHELIAL GROWTH FACTOR A;

EID: 84928038747     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1420380112     Document Type: Article

References (40)

1. Wells JA, McClendon CL (2007) Reaching for high-hanging fruit in drug discovery at protein-protein interfaces. Nature 450(7172):1001-1009.
2. Arkin MR, Tang Y, Wells JA (2014) Small-molecule inhibitors of protein-protein interactions: Progressing toward the reality. Chem Biol 21(9):1102-1114.
3. Wilson AJ (2009) Inhibition of protein-protein interactions using designed molecules. Chem Soc Rev 38(12):3289-3300.
4. Vlieghe P, Lisowski V, Martinez J, Khrestchatisky M (2010) Synthetic therapeutic peptides: Science and market. Drug Discov Today 15(1-2):40-56.
5. Kariolis MS, Kapur S, Cochran JR (2013) Beyond antibodies: Using biological principles to guide the development of next-generation protein therapeutics. Curr Opin Biotechnol 24(6):1072-1077.
6. Johnson LM, Gellman SH (2013) α-Helix mimicry with α/β-peptides. Methods Enzymol 523:407-429.
7. Horne WS, et al. (2009) Structural and biological mimicry of protein surface recognition by α/β-peptide foldamers. Proc Natl Acad Sci USA 106(35):14751-14756.
8. Cheloha RW, Maeda A, Dean T, Gardella TJ, Gellman SH (2014) Backbone modification of a polypeptide drug alters duration of action in vivo. Nat Biotechnol 32(7):653-655.
9. Johnson LM, et al. (2014) A potent α/β-peptide analogue of GLP-1 with prolonged action in vivo. J Am Chem Soc 136(37):12848-12851.
10. Lo Conte L, Chothia C, Janin J (1999) The atomic structure of protein-protein recognition sites. J Mol Biol 285(5):2177-2198.
11. Binz HK, Amstutz P, Plückthun A (2005) Engineering novel binding proteins from nonimmunoglobulin domains. Nat Biotechnol 23(10):1257-1268.
12. Grönwall C, Ståhl S (2009) Engineered affinity proteins - generation and applications. J Biotechnol 140(3-4):254-269.
13. Moore SJ, et al. (2013) Engineered knottin peptide enables noninvasive optical imaging of intracranial medulloblastoma. Proc Natl Acad Sci USA 110(36):14598-14603.
14. Löfblom J, et al. (2010) Affibody molecules: Engineered proteins for therapeutic, diagnostic and biotechnological applications. FEBS Lett 584(12):2670-2680.
15. Deisenhofer J (1981) Crystallographic refinement and atomic models of a human Fc fragment and its complex with fragment B of protein A from Staphylococcus aureus at 2.9- and 2.8-Å resolution. Biochemistry 20(9):2361-2370.
16. Nilsson B, et al. (1987) A synthetic IgG-binding domain based on staphylococcal protein A. Protein Eng 1(2):107-113.
17. Tashiro M, et al. (1997) High-resolution solution NMR structure of the Z domain of staphylococcal protein A. J Mol Biol 272(4):573-590.
18. Nord K, et al. (1997) Binding proteins selected from combinatorial libraries of an α-helical bacterial receptor domain. Nat Biotechnol 15(8):772-777.
19. Fedorova A, et al. (2011) The development of peptide-based tools for the analysis of angiogenesis. Chem Biol 18(7):839-845.
20. Jonsson A, Wållberg H, Herne N, Ståhl S, Frejd FY (2009) Generation of tumour-necrosis-factor-α-specific affibody molecules capable of blocking receptor binding in vitro. Biotechnol Appl Biochem 54(2):93-103.
21. Orlova A, et al. (2006) Tumor imaging using a picomolar affinity HER2 binding affibody molecule. Cancer Res 66(8):4339-4348.
22. Baum RP, et al. (2010) Molecular imaging of HER2-expressing malignant tumors in breast cancer patients using synthetic 111In- or 68Ga-labeled affibody molecules. J Nucl Med 51(6):892-897.
23. Henchey LK, Jochim AL, Arora PS (2008) Contemporary strategies for the stabilization of peptides in the α-helical conformation. Curr Opin Chem Biol 12(6):692-697.
24. Braisted AC, Wells JA (1996) Minimizing a binding domain from protein A. Proc Natl Acad Sci USA 93(12):5688-5692.
25. Starovasnik MA, Braisted AC, Wells JA (1997) Structural mimicry of a native protein by a minimized binding domain. Proc Natl Acad Sci USA 94(19):10080-10085.
26. Webster JM, Zhang R, Gambhir SS, Cheng Z, Syud FA (2009) Engineered two-helix small proteins for molecular recognition. ChemBioChem 10(8):1293-1296.
27. Ferrara N, Gerber HP, LeCouter J (2003) The biology of VEGF and its receptors. Nat Med 9(6):669-676.
28. Ferrara N, Kerbel RS (2005) Angiogenesis as a therapeutic target. Nature 438(7070):967-974.
29. Carmeliet P, Jain RK (2011) Molecular mechanisms and clinical applications of angiogenesis. Nature 473(7347):298-307.
30. Grothey A, Galanis E (2009) Targeting angiogenesis: Progress with anti-VEGF treatment with large molecules. Nat Rev Clin Oncol 6(9):507-518.
31. Wiesmann C, et al. (1997) Crystal structure at 1.7 Å resolution of VEGF in complex with domain 2 of the Flt-1 receptor. Cell 91(5):695-704.
32. Peterson KJ, et al. (2008) A fluorescence polarization assay for identifying ligands that bind to vascular endothelial growth factor. Anal Biochem 378(1):8-14.
33. Karle IL, Balaram P (1990) Structural characteristics of α-helical peptide molecules containing Aib residues. Biochemistry 29(29):6747-6756.
34. Yamaguchi H, et al. (2003) Effect of α,α-dialkyl amino acids on the protease resistance of peptides. Biosci Biotechnol Biochem 67(10):2269-2272.
35. Haase HS, et al. (2012) Extending foldamer design beyond α-helix mimicry: α/β-Peptide inhibitors of vascular endothelial growth factor signaling. J Am Chem Soc 134(18):7652-7655.
36. Fairbrother WJ, et al. (1998) Novel peptides selected to bind vascular endothelial growth factor target the receptor-binding site. Biochemistry 37(51):17754-17764.
37. Beenken A, Mohammadi M (2009) The FGF family: Biology, pathophysiology and therapy. Nat Rev Drug Discov 8(3):235-253.
38. Eigenbrot C, Ultsch M, Dubnovitsky A, Abrahmsén L, Härd T (2010) Structural basis for high-affinity HER2 receptor binding by an engineered protein. Proc Natl Acad Sci USA 107(34):15039-15044.
39. Locksley RM, Killeen N, Lenardo MJ (2001) The TNF and TNF receptor superfamilies: Integrating mammalian biology. Cell 104(4):487-501.
40. Palladino MA, Bahjat FR, Theodorakis EA, Moldawer LL (2003) Anti-TNF-α therapies: The next generation. Nat Rev Drug Discov 2(9):736-746.