Analysis the Constrained Peptide that Inhibit HIV-1 Entry by Simulation

摘要

Synthetic peptides derived from the C peptide inhibit HIV-1 entry. Both C-peptides (C14wt and C141ink) were docked manually to the hydrophobic pocket of gp41 based on the structural information of N-terminal using AutoDock 3.0. The molecular dynamics simulations were carried out in water using GROMACS 3.0. The analysis results show that there is a relationship between the inhibitory potency and the stability of corresponding helix. Three residues from the C14wt and two residues from the C141ink insert into the hydrophobic pocket of gp41 and make extensive hydrophobic contacts. Results provide strong evidence that the use of the crosslinker can improve the helix stabilization and the inhibitory potency.