Structure-based de novo design, synthesis, and biological evaluation of the indole-based PPARgamma ligands (I).

MCSS and LeapFrog, two de novo drug design programs, were used for the novel indole-based PPARgamma ligands' study. The designed compounds were synthesized and tested for the PPARgamma protein binding activities in vitro. Out of the compounds that were synthesized, two molecules (compounds 14d and 7d) possessed potent PPARgamma protein binding activity close to rosiglitazone in vitro.