Molecular dynamics analysis of a docking-derived baicalein–PPARγ ligand-binding-domain model suggests a pocket-associated AF-2-anchor-silent ensemble

Abstract

Baicalein was examined in a selected docking-derived peroxisome proliferator-activated receptor γ (PPARγ) ligand-binding-domain (LBD) model to test whether pocket association, local helix 12 (H12) organization, and canonical activation function-2 (AF-2) anchoring were coupled under the sampled simulation conditions. Because no baicalein-bound PPARγ cocrystal structure was used, the results are interpreted as a selected-pose molecular dynamics model rather than as a definitive experimental binding mode. Three independent 100-ns replicas were analyzed with bound-state filtering, H12 and AF-2 descriptors, arm-resolved energetic decomposition, interaction fingerprints, a local Tyr473-engagement potential of mean force (PMF), and exploratory state annotation. Baicalein remained spatially associated with the ligand-binding pocket by the minimum-distance and center-of-mass criteria, whereas pocket-shell contact persistence was replica-dependent, with retained fractions of 94.20%, 94.00%, and 71.64% in replicas 1–3. Within bound-state-filtered frames and under the selected neutral baicalein/HIE histidine model, direct ligand hydrogen bonds to Ser289, His323, His449, and Tyr473 were not detected, and the AF-2 anchor-panel union occupancy was 0.00%. This anchor-negative pattern occurred despite measurable local H12 order, indicating that local H12 structural persistence and canonical AF-2 anchor assembly were separable in the selected model. Arm-resolved molecular mechanics/generalized Born surface area (MM/GBSA) descriptors and ProLIF fingerprints supported mixed Arm II/Arm III participation, with recurrent van der Waals contacts involving Cys285, Ile341, Leu330, Leu333, Arg288, and Ile326. The local Tyr473 PMF favored a displaced baicalein geometry, with a minimum at 0.66 nm along the Tyr473 hydroxyl-to-ligand-acceptor coordinate. Limited ligand-protonation and His323/His449-tautomer sensitivity screens did not recover persistent canonical AF-2 anchoring under the tested short-screen conditions. Exploratory state analysis resolved in-pocket heterogeneity but did not identify a descriptor-supported state with persistent canonical AF-2 anchoring. These simulations support a constrained structural model in which baicalein samples a pocket-associated, measurably H12-organized, anchor-negative PPARγ ensemble stabilized by non-canonical pocket interactions. The interpretation is limited to simulation descriptors and does not establish receptor activation, partial agonism, phosphorylation regulation, or transcriptional output.