Structural insights for the design of new PPARgamma partial agonists with high binding affinity and low transactivation activity

J Comput Aided Mol Des. 2011 Aug;25(8):717-28. doi: 10.1007/s10822-011-9446-9. Epub 2011 Jun 21.


Peroxisome Proliferator-Activated Receptor γ (PPARγ) full agonists are molecules with powerful insulin-sensitizing action that are used as antidiabetic drugs. Unfortunately, these compounds also present various side effects. Recent results suggest that effective PPARγ agonists should show a low transactivation activity but a high binding affinity to inhibit phosphorylation at Ser273. We use several structure activity relationship studies of synthetic PPARγ agonists to explore the different binding features of full and partial PPARγ agonists with the aim of differentiating the features needed for binding and those needed for the transactivation activity of PPARγ. Our results suggest that effective partial agonists should have a hydrophobic moiety and an acceptor site with an appropriate conformation to interact with arm II and establish a hydrogen bond with Ser342 or an equivalent residue at arm III. Despite the fact that interactions with arm I increase the binding affinity, this region should be avoided in order to not increase the transactivation activity of potential PPARγ partial agonists.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Binding Sites
  • Cluster Analysis*
  • Computer Simulation
  • Drug Design*
  • Hypoglycemic Agents / agonists
  • Hypoglycemic Agents / chemistry*
  • Hypoglycemic Agents / metabolism
  • Ligands
  • Models, Molecular*
  • Molecular Conformation
  • PPAR gamma / agonists*
  • PPAR gamma / chemistry*
  • PPAR gamma / metabolism
  • Quantitative Structure-Activity Relationship*
  • Thiazolidinediones / chemistry


  • Hypoglycemic Agents
  • Ligands
  • PPAR gamma
  • Thiazolidinediones