Structure-Based Stepwise Screening of PPARγ Antagonists as Potential Competitors with NCOA1 Coactivator Peptide for PPARγ CIS Site

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The small-molecule modulators (agonists and antagonists) of peroxisome proliferator-activated receptor-γ (PPARγ) have been widely used to treat metabolic, cardiovascular and inflammatory diseases such as Type-2 diabetes and heart failure. Existing PPARγ modulators are all developed to target the ligand-binding site (LBS) in PPARγ ligand-binding domain (LBD) interior, where is spatially separated from the coactivator-interacting site (CIS) on PPARγ LBD surface and can thus only indirectly mediate the binding of NCOA1 coactivator peptide to CIS site. Here, we propose a new therapeutic strategy termed as Type-III PPARγ antagonists, which competitively disrupt the NCOA1 peptide binding by directly targeting PPARγ CIS site. Such antagonists are also known as inverse agonists that can partially or fully repress the basal transcriptional activity of PPARγ. A structure-based stepwise screening is performed against a purchasable biogenic compound library to identify CIS-specific binding competitors. The screening integrates empirical manual exclusion, druglikeness/pharmacokinetic evaluation, chemical similarity analysis and high-throughput molecular docking to rank the relative binding capability for compound candidate lists. The competitive potency of eight promising hits against a truncated version (core binding sequence) of full-length NCOA1 peptide (685ERHKILHRLLQEGSPS700) is tested using fluorescence competition assays. Consequently, two out of the eight tested compounds are determined as potential competitors with NCOA1 peptide for PPARγ CIS site, with CC50 values of 13 ± 1.8 and 54 ± 6.7 μM, respectively. Structural analysis reveals that the two competitor ligands are anchored at the central hole of CIS site through their substituted phenyl moieties, while forming a variety of hydrogen bonds, cation-π stacking and hydrophobic contacts with the regions surrounding the hole, conferring both stability and specificity to the CIS–competitor recognition and interaction.