Abstract
An in silico peptide design strategy is conducted in order to introduce a novel series of pertuzumab mimetic peptides, aimed to target the extracellular domain of HER-2 and prevent its signal transduction. A combination of alanine scanning and contact surface analysis is employed to assess the pertuzumab paratope, HER-2 epitope and their hot spots. Furthermore, the recognised residues are utilised to construct nine 10-mer peptides. Some of the peptides are modified pertuzumab paratope sequences, whereas the others are designed and modified as strongly binding complementary peptides for HER-2 epitope. Evaluation of the peptides is carried out through homology modelling, molecular dynamics simulation (MDS) and docking. It was revealed that all peptides mimic pertuzumab performance since they exhibit noticeable binding interaction energies, inhibitory efficiencies and number of hot spots. However, YNDSTHGERL with five hot spots and considerable interaction energy has the highest ability in interfering with HER-2-specific epitope. Inhibiting potency of this peptide is verified through MDSs.
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