Integrated Virtual Screening for the Identification of Novel and Selective Peroxisome Proliferator-Activated Receptor (PPAR) Scaffolds

We describe a fully customizable and integrated target-specific
“tiered” virtual screening approach tailored to identifying
and characterizing novel peroxisome proliferator activated receptor
γ (PPARγ) scaffolds. Built on structure- and ligand-based
computational techniques, a consensus protocol was developed for use
in the virtual screening of chemical databases, focused toward retrieval
of novel bioactive chemical scaffolds for PPARγ. Consequent
from application, three novel PPAR scaffolds displaying distinct chemotypes
have been identified, namely, 5-(4-(benzyloxy)-3-chlorobenzylidene)­dihydro-2-thioxopyrimidine-4,6­(1H,5H)-dione (MDG 548), 3-((4-bromophenoxy)­methyl)-N-(4-nitro-1H-pyrazol-1-yl)­benzamide (MDG
559), and ethyl 2-[3-hydroxy-5-(5-methyl-2-furyl)-2-oxo-4-(2-thienylcarbonyl)-2,5-dihydro-1H-pyrrol-1-yl]-4-methyl-1,3-thiazole-5-carboxylate
(MDG 582). Fluorescence polarization (FP) and time resolved fluorescence
resonance energy transfer (TR-FRET) show that these compounds display
high affinity competitive binding to the PPARγ-LBD (EC50 of 215 nM to 5.45 μM). Consequent characterization by a TR-FRET
activation reporter assay demonstrated agonism of PPARγ by all
three compounds (EC50 of 467–594nM). Additionally,
differential PPAR isotype specificity was demonstrated through assay
against PPARα and PPARδ subtypes. This work showcases
the ability of target specific “tiered screen” protocols
to successfully identify novel scaffolds of individual receptor subtypes
with greater efficacy than isolated screening methods.