Abstract
Molecular docking,molecular dynamics(MD) simulation and molecular mechanics Poisson-Boltzmann surface area(MM-PBSA)/molecular mechanics Generalized Born surface area(MM-GBSA) analysis are applied to predict the binding mode of two N-substituted pyrrole derivate inhibitors to the hydrophobic pocket in HIV-1 envelope protein gp41.Taking into account the flexibility of the receptor,multiple receptor conformations are used in docking with the ligands,which results in several possible binding modes.MD simulations and MM-PBSA binding energy calculations are performed on all the binding modes to identify the most favorable binding estimate.The MM-PBSA results indicate that the binding is mainly driven by non-polar interactions,while polar interactions determine the orientation of the ligands binding into the target site.Further analysis reveals the key residues and ligand-receptor interactions which contribute significantly to the binding affinity.This study provides useful information for rational design and optimization of N-substituted pyrrole derivatives as HIV-1 fusion inhibitors.
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