Structure-based design, synthesis, and characterization of dual hotspot small-molecule HIV-1 entry inhibitors

J Med Chem. 2012 May 10;55(9):4382-96. doi: 10.1021/jm300265j. Epub 2012 Apr 23.


Cellular infection by HIV-1 is initiated with a binding event between the viral envelope glycoprotein gp120 and the cellular receptor protein CD4. The CD4-gp120 interface is dominated by two hotspots: a hydrophobic gp120 cavity capped by Phe43(CD4) and an electrostatic interaction between residues Arg59(CD4) and Asp368(gp120). The CD4 mimetic small-molecule NBD-556 (1) binds within the gp120 cavity; however, 1 and related congeners demonstrate limited viral neutralization breadth. Herein, we report the design, synthesis, characterization, and X-ray structures of gp120 in complex with small molecules that simultaneously engage both binding hotspots. The compounds specifically inhibit viral infection of 42 tier 2 clades B and C viruses and are shown to be antagonists of entry into CD4-negative cells. Dual hotspot design thus provides both a means to enhance neutralization potency of HIV-1 entry inhibitors and a novel structural paradigm for inhibiting the CD4-gp120 protein-protein interaction.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, N.I.H., Intramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • CD4 Antigens / metabolism
  • Calorimetry / methods
  • Crystallography, X-Ray
  • HIV Envelope Protein gp120 / metabolism
  • HIV Fusion Inhibitors / chemical synthesis
  • HIV Fusion Inhibitors / chemistry*
  • HIV Fusion Inhibitors / pharmacology*
  • HIV Infections / drug therapy*
  • HIV Infections / metabolism
  • HIV Infections / virology
  • HIV-1 / physiology*
  • Humans
  • Indans / chemical synthesis
  • Indans / chemistry*
  • Indans / pharmacology*
  • Inhibitory Concentration 50
  • Magnetic Resonance Spectroscopy
  • Mass Spectrometry
  • Models, Molecular
  • Molecular Dynamics Simulation
  • Neutralization Tests / methods
  • Structure-Activity Relationship
  • Thermodynamics
  • Virus Internalization / drug effects


  • CD4 Antigens
  • HIV Envelope Protein gp120
  • HIV Fusion Inhibitors
  • Indans

Associated data

  • PDB/4DKO
  • PDB/4DKP
  • PDB/4DKQ
  • PDB/4DKR