The energy landscape of a selective tumor-homing pentapeptide

J Phys Chem B. 2008 Jul 24;112(29):8692-700. doi: 10.1021/jp711477k. Epub 2008 Jun 28.

Abstract

Recently, a potentially powerful strategy based on phage-display libraries has been presented to target tumors via homing peptides attached to nanoparticles. The Cys-Arg-Glu-Lys-Ala (CREKA) peptide sequence has been identified as a tumor-homing peptide that binds to clotted plasmas proteins present in tumor vessels and interstitium. The aim of this work consists of mapping the conformational profile of CREKA to identify the bioactive conformation. For this purpose, a conformational search procedure based on modified simulated annealing combined with molecular dynamics was applied to three systems that mimic the experimentally used conditions: (i) the free peptide; (ii) the peptide attached to a nanoparticle; and (iii) the peptide inserted in a phage display protein. In addition, the free peptide was simulated in an ionized aqueous solution environment, which mimics the ionic strength of the physiological medium. Accessible minima of all simulated systems reveal a multiple interaction pattern involving the ionized side chains of Arg, Glu, and Lys, which induces a beta-turn motif in the backbone observed in all simulated CREKA systems.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, N.I.H., Intramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Arginine / chemistry
  • Arginine / metabolism
  • Binding Sites
  • Computer Simulation
  • Glutamic Acid / chemistry
  • Glutamic Acid / metabolism
  • Lysine / chemistry
  • Lysine / metabolism
  • Molecular Sequence Data
  • Nanoparticles / chemistry
  • Neoplasm Proteins / chemistry*
  • Neoplasm Proteins / metabolism
  • Oligopeptides / chemistry*
  • Oligopeptides / metabolism
  • Peptide Fragments / chemistry*
  • Peptide Fragments / metabolism
  • Protein Structure, Secondary
  • Solutions / chemistry
  • Thermodynamics
  • Time Factors
  • Water / chemistry

Substances

  • Neoplasm Proteins
  • Oligopeptides
  • Peptide Fragments
  • Solutions
  • Water
  • Glutamic Acid
  • Arginine
  • Lysine