Computational characterization of binding of small molecule inhibitors to HIV-1 gp41

Kuizhong Song, Ju Bao, Yueming Sun, John Z.H. Zhang

Research output: Contribution to journalArticlepeer-review


Developing orally available small molecule inhibitors of HIV-1 fusion has attracted significant interest over many years. Frey had recently reported several synthetic compounds which are experimentally shown to inhibit cell-cell fusion in the low micromolar range. We carried out computational study to help identify possible binding modes by docking these compounds onto the hydrophobic pocket on gp41 and to characterize structures of binding complexes. The detailed gp41-molecule binding interactions and free energies of binding are obtained through molecular dynamics simulation and MM-PBSA calculation. Specific molecular interactions in the gp41-inhibitor complexes are identified. The present computational study complements the corresponding experimental investigation and helps establish a good starting point for further refinement of small molecular gp41 inhibitors.

Original languageEnglish (US)
Pages (from-to)1307-1311
Number of pages5
JournalChinese Journal of Chemistry
Issue number7
StatePublished - Jul 2011


  • HIV-1 entry inhibition
  • binding free energy
  • binding mode
  • molecular dynamics
  • protein

ASJC Scopus subject areas

  • General Chemistry


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