A New Class of Allosteric HIV-1 Integrase Inhibitors Identified by Crystallographic Fragment Screening of the Catalytic Core Domain

J Biol Chem. 2016 Nov 4;291(45):23569-23577. doi: 10.1074/jbc.M116.753384. Epub 2016 Sep 19.


HIV-1 integrase (IN) is essential for virus replication and represents an important multifunctional therapeutic target. Recently discovered quinoline-based allosteric IN inhibitors (ALLINIs) potently impair HIV-1 replication and are currently in clinical trials. ALLINIs exhibit a multimodal mechanism of action by inducing aberrant IN multimerization during virion morphogenesis and by competing with IN for binding to its cognate cellular cofactor LEDGF/p75 during early steps of HIV-1 infection. However, quinoline-based ALLINIs impose a low genetic barrier for the evolution of resistant phenotypes, which highlights a need for discovery of second-generation inhibitors. Using crystallographic screening of a library of 971 fragments against the HIV-1 IN catalytic core domain (CCD) followed by a fragment expansion approach, we have identified thiophenecarboxylic acid derivatives that bind at the CCD-CCD dimer interface at the principal lens epithelium-derived growth factor (LEDGF)/p75 binding pocket. The most active derivative (5) inhibited LEDGF/p75-dependent HIV-1 IN activity in vitro with an IC50 of 72 μm and impaired HIV-1 infection of T cells at an EC50 of 36 μm The identified lead compound, with a relatively small molecular weight (221 Da), provides an optimal building block for developing a new class of inhibitors. Furthermore, although structurally distinct thiophenecarboxylic acid derivatives target a similar pocket at the IN dimer interface as the quinoline-based ALLINIs, the lead compound, 5, inhibited IN mutants that confer resistance to quinoline-based compounds. Collectively, our findings provide a plausible path for structure-based development of second-generation ALLINIs.

Keywords: HIV-1; HIV-1 integrase; X-ray crystallography; allosteric inhibitor; drug discovery; drug screening; fragment screening; human immunodeficiency virus (HIV); integrase; medicinal chemistry.

MeSH terms

  • Allosteric Regulation / drug effects
  • Carboxylic Acids / chemistry
  • Carboxylic Acids / pharmacology
  • Catalytic Domain / drug effects
  • Crystallography, X-Ray
  • Drug Discovery
  • HEK293 Cells
  • HIV Infections / drug therapy*
  • HIV Infections / virology
  • HIV Integrase / chemistry
  • HIV Integrase / metabolism*
  • HIV Integrase Inhibitors / chemistry*
  • HIV Integrase Inhibitors / pharmacology*
  • HIV-1 / drug effects*
  • Humans
  • Models, Molecular
  • Molecular Docking Simulation
  • Thiophenes / chemistry*
  • Thiophenes / pharmacology*


  • Carboxylic Acids
  • HIV Integrase Inhibitors
  • Thiophenes
  • HIV Integrase
  • p31 integrase protein, Human immunodeficiency virus 1

Associated data

  • PDB/5KRS
  • PDB/5KRT
  • PDB/4IDL
  • PDB/4TSX