Investigation on the sucrose binding pocket of HIV-1 Integrase by molecular dynamics and synergy experiments

Bioorg Med Chem Lett. 2015 Aug 1;25(15):3013-6. doi: 10.1016/j.bmcl.2015.05.011. Epub 2015 May 15.

Abstract

Enzymes whose catalytic activity depends on multimeric assembly are targets for inhibitors that perturb the interactions between the protein subunits such as the HIV-1 Integrase (IN). Sucrose has been recently crystallized in complex with IN revealing an allosteric binding pocket at the monomer-monomer interface. Herein, molecular dynamics were applied to theoretically test the effect of this small ligand on IN. As a result, such a compound increases the mutual free energy of binding between the two interacting monomers. Biological experiments confirmed the computational forecast.

Keywords: HIV-1 Integrase; Molecular dynamics; Protein–protein interaction; Sucrose.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites
  • Drug Synergism
  • HIV Infections / drug therapy
  • HIV Infections / virology
  • HIV Integrase / chemistry
  • HIV Integrase / metabolism*
  • HIV Integrase Inhibitors / pharmacology*
  • HIV-1 / drug effects
  • HIV-1 / enzymology*
  • Humans
  • Molecular Docking Simulation
  • Molecular Dynamics Simulation
  • Protein Binding
  • Protein Multimerization / drug effects
  • Raltegravir Potassium / pharmacology
  • Sucrose / pharmacology*
  • Thermodynamics

Substances

  • HIV Integrase Inhibitors
  • Raltegravir Potassium
  • Sucrose
  • HIV Integrase
  • p31 integrase protein, Human immunodeficiency virus 1