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Solution structure of a phage-derived peptide antagonist in complex with vascular endothelial growth factor.

Pan B, Li B, Russell SJ, Tom JY, Cochran AG, Fairbrother WJ
J Mol Biol 316 769-87 (2002)
Cited: 34 times
EuropePMC logo PMID: 11866530

Abstract

Vascular endothelial growth factor (VEGF) is a potent endothelial cell-specific mediator of angiogenesis and vasculogenesis. VEGF is involved pathologically in cancer, proliferative retinopathy and rheumatoid arthritis, and as such represents an important therapeutic target. Three classes of disulfide-constrained peptides that antagonize binding of the VEGF dimer to its receptors, KDR and Flt-1, were identified previously using phage display methods. NMR studies of a representative peptide from the most potent class of these peptide antagonists, v107 (GGNECDAIRMWEWECFERL), were undertaken to characterize its interactions with VEGF. v107 has no defined structure free in solution, but binding to VEGF induces folding of the peptide. The solution structure of the VEGF receptor-binding domain-v107 complex was determined using 3940 (1970 per VEGF monomer) internuclear distance and 476 (238 per VEGF monomer) dihedral angle restraints derived from NMR data obtained using samples containing either (13)C/(15)N-labeled protein plus excess unlabeled peptide or (13)C/(15)N-labeled peptide plus excess unlabeled protein. Residual dipolar coupling restraints supplemented the structure determination of the complex and were found to increase significantly both the global precision of VEGF in the complex and the agreement with available crystal structures of VEGF. The calculated ensemble of structures is of high precision and is in excellent agreement with the experimental restraints. v107 has a turn-helix conformation with hydrophobic residues partitioned to one face of the peptide and polar or charged residues at the other face. Contacts between two v107 peptides and the VEGF dimer are mediated by primarily hydrophobic side-chain interactions. The v107-binding site on VEGF overlaps partially with the binding site of KDR and is similar to that for domain 2 of Flt-1. The structure of the VEGF-v107 complex provides new insight into how binding to VEGF can be achieved that may be useful for the design of small molecule antagonists.

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  2. A Structural Overview of Vascular Endothelial Growth Factors Pharmacological Ligands: From Macromolecules to Designed Peptidomimetics. Ye X, Gaucher JF, Vidal M, Broussy S. Molecules 26 (2021)
  3. Unnatural helical peptidic foldamers as protein segment mimics. Sang P, Cai J. Chem Soc Rev 52 4843-4877 (2023)

Articles - 1kat mentioned but not cited (5)

  1. Extending foldamer design beyond α-helix mimicry: α/β-peptide inhibitors of vascular endothelial growth factor signaling. Haase HS, Peterson-Kaufman KJ, Lan Levengood SK, Checco JW, Murphy WL, Gellman SH. J Am Chem Soc 134 7652-7655 (2012)
  2. Combined Use of Oligopeptides, Fragment Libraries, and Natural Compounds: A Comprehensive Approach To Sample the Druggability of Vascular Endothelial Growth Factor. Bayó-Puxan N, Rodríguez-Mias R, Goldflam M, Kotev M, Ciudad S, Hipolito CJ, Varese M, Suga H, Campos-Olivas R, Barril X, Guallar V, Teixidó M, García J, Giralt E. ChemMedChem 11 928-939 (2016)
  3. Clustering of disulfide-rich peptides provides scaffolds for hit discovery by phage display: application to interleukin-23. Barkan DT, Cheng XL, Celino H, Tran TT, Bhandari A, Craik CS, Sali A, Smythe ML. BMC Bioinformatics 17 481 (2016)
  4. Enhancing peptide ligand binding to vascular endothelial growth factor by covalent bond formation. Marquez BV, Beck HE, Aweda TA, Phinney B, Holsclaw C, Jewell W, Tran D, Day JJ, Peiris MN, Nwosu C, Lebrilla C, Meares CF. Bioconjug Chem 23 1080-1089 (2012)
  5. Structural and ITC Characterization of Peptide-Protein Binding: Thermodynamic Consequences of Cyclization Constraints, a Case Study on Vascular Endothelial Growth Factor Ligands. Gaucher JF, Reille-Seroussi M, Broussy S. Chemistry 28 e202200465 (2022)


Reviews citing this publication (5)

  1. The role of VEGF receptors in angiogenesis; complex partnerships. Cébe-Suarez S, Zehnder-Fjällman A, Ballmer-Hofer K. Cell Mol Life Sci 63 601-615 (2006)
  2. Molecular and functional diversity of vascular endothelial growth factors. Yamazaki Y, Morita T. Mol Divers 10 515-527 (2006)
  3. Residual dipolar couplings in NMR structure analysis. Lipsitz RS, Tjandra N. Annu Rev Biophys Biomol Struct 33 387-413 (2004)
  4. Exploring protein-protein interactions with phage display. Sidhu SS, Fairbrother WJ, Deshayes K. Chembiochem 4 14-25 (2003)
  5. Peptide-based molecules in angiogenesis. D'Andrea LD, Del Gatto A, Pedone C, Benedetti E. Chem Biol Drug Des 67 115-126 (2006)

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  2. Targeting angiogenesis: structural characterization and biological properties of a de novo engineered VEGF mimicking peptide. D'Andrea LD, Iaccarino G, Fattorusso R, Sorriento D, Carannante C, Capasso D, Trimarco B, Pedone C. Proc Natl Acad Sci U S A 102 14215-14220 (2005)
  3. Identification of a small peptide that inhibits PCSK9 protein binding to the low density lipoprotein receptor. Zhang Y, Eigenbrot C, Zhou L, Shia S, Li W, Quan C, Tom J, Moran P, Di Lello P, Skelton NJ, Kong-Beltran M, Peterson A, Kirchhofer D. J Biol Chem 289 942-955 (2014)
  4. Rapid identification of small binding motifs with high-throughput phage display: discovery of peptidic antagonists of IGF-1 function. Deshayes K, Schaffer ML, Skelton NJ, Nakamura GR, Kadkhodayan S, Sidhu SS. Chem Biol 9 495-505 (2002)
  5. Bacterial display enables efficient and quantitative peptide affinity maturation. Kenrick SA, Daugherty PS. Protein Eng Des Sel 23 9-17 (2010)
  6. Disulfide bonds versus TrpTrp pairs in irregular beta-hairpins: NMR structure of vammin loop 3-derived peptides as a case study. Mirassou Y, Santiveri CM, Pérez de Vega MJ, González-Muñiz R, Jiménez MA. Chembiochem 10 902-910 (2009)
  7. Identification of peptide mimetics of xenoreactive alpha-Gal antigenic epitope by phage display. Lang J, Zhan J, Xu L, Yan Z. Biochem Biophys Res Commun 344 214-220 (2006)
  8. A fluorescence polarization assay for identifying ligands that bind to vascular endothelial growth factor. Peterson KJ, Sadowsky JD, Scheef EA, Pal S, Kourentzi KD, Willson RC, Bresnick EH, Sheibani N, Gellman SH. Anal Biochem 378 8-14 (2008)
  9. Peptide ligands that use a novel binding site to target both TGF-β receptors. Li L, Orner BP, Huang T, Hinck AP, Kiessling LL. Mol Biosyst 6 2392-2402 (2010)
  10. Helical peptides from VEGF and Vammin hotspots for modulating the VEGF-VEGFR interaction. García-Aranda MI, González-López S, Santiveri CM, Gagey-Eilstein N, Reille-Seroussi M, Martín-Martínez M, Inguimbert N, Vidal M, García-López MT, Jiménez MA, González-Muñiz R, Pérez de Vega MJ. Org Biomol Chem 11 1896-1905 (2013)
  11. Amino acid determinants of beta-hairpin conformation in erythropoeitin receptor agonist peptides derived from a phage display library. Skelton NJ, Russell S, de Sauvage F, Cochran AG. J Mol Biol 316 1111-1125 (2002)
  12. Parallel solid-phase synthesis of a small library of linear and hydrocarbon-bridged analogues of VEGF(81-91): potential biological tools for studying the VEGF/VEGFR-1 interaction. García-Aranda MI, Marrero P, Gautier B, Martín-Martínez M, Inguimbert N, Vidal M, García-López MT, Jiménez MA, González-Muñiz R, Pérez de Vega MJ. Bioorg Med Chem 19 1978-1986 (2011)
  13. The binding mechanism of a peptidic cyclic serine protease inhibitor. Jiang L, Svane AS, Sørensen HP, Jensen JK, Hosseini M, Chen Z, Weydert C, Nielsen JT, Christensen A, Yuan C, Jensen KJ, Nielsen NC, Malmendal A, Huang M, Andreasen PA. J Mol Biol 412 235-250 (2011)
  14. Dynamical behavior of the vascular endothelial growth factor: biological implications. Horta BA, Cirino JJ, de Alencastro RB. Proteins 67 517-525 (2007)
  15. Iterative Nonproteinogenic Residue Incorporation Yields α/β-Peptides with a Helix-Loop-Helix Tertiary Structure and High Affinity for VEGF. Checco JW, Gellman SH. Chembiochem 18 291-299 (2017)
  16. Molecular recognition at protein surface in solution and gas phase: Five VEGF peptidic ligands show inverse affinity when studied by NMR and CID-MS. Dyachenko A, Goldflam M, Vilaseca M, Giralt E. Biopolymers 94 689-700 (2010)
  17. On the structure, interactions, and dynamics of bound VEGF. Horta BA, Cirino JJ, de Alencastro RB. J Mol Graph Model 26 1091-1103 (2008)
  18. Screening and identification of a novel target specific for hepatoma cell line HepG2 from the FliTrx bacterial peptide library. Li W, Lei P, Yu B, Wu S, Peng J, Zhao X, Zhu H, Kirschfink M, Shen G. Acta Biochim Biophys Sin (Shanghai) 40 443-451 (2008)
  19. Biophysical Studies of the Induced Dimerization of Human VEGF Receptor 1 Binding Domain by Divalent Metals Competing with VEGF-A. Gaucher JF, Reille-Seroussi M, Gagey-Eilstein N, Broussy S, Coric P, Seijo B, Lascombe MB, Gautier B, Liu WQ, Huguenot F, Inguimbert N, Bouaziz S, Vidal M, Broutin I. PLoS One 11 e0167755 (2016)
  20. Identification and characterization of peptide probes directed against PKCalpha conformations. Ashraf SS, Anderson E, Duke K, Hamilton PT, Fredericks Z. J Pept Res 61 263-273 (2003)
  21. VEGFR1 domain 2 covalent labeling with horseradish peroxidase: Development of a displacement assay on VEGF. Reille-Seroussi M, Gaucher JF, Cussac LA, Broutin I, Vidal M, Broussy S. Anal Biochem 530 107-112 (2017)


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