Repurposing dual-C-prenylated flavonoids as potent allosteric inhibitors of PTP1B: Integrated phytochemical, enzymological, and in silico evidence

Abstract

Protein-tyrosine phosphatase 1B (PTP1B) is a master negative regulator of insulin and leptin signaling, yet clinically useful inhibitors remain elusive. Guided by a repurposing strategy, we investigated Tephrosia villosa as a natural source of PTP1B modulators. Chromatographic fractionation of the aerial parts afforded nine flavonoids and related phenolics, whose structures were elucidated by spectroscopic tools. Enzymatic screening revealed that the diprenylated isoflavonoids 6,8-diprenylgenistein and 6,8-diprenylnaringenin inhibit recombinant PTP1B with sub-micromolar potency (IC₅₀ ≈ 1 μM) and non-competitive kinetics, outperforming the reference inhibitor ursolic acid six-fold. Molecular docking and 200 ns molecular dynamics simulations located both ligands in the hydrophobic α3/α7 allosteric pocket, where dual C-prenyl chains engage an aromatic clamp formed by Phe196 and Phe280; MM/PBSA binding energies (≈ −30 kcal mol⁻¹) and a single deep free-energy basin corroborate tight, entropy-driven binding that locks the WPD loop open. Free energy landscape analysis funnels these trajectories into a single deep basin, confirming that ligand binding rigidifies the WPD-loop in an open, catalytically inactive conformation. ADMET predictions show high oral absorption, no Lipinski violations and minimal cardiotoxic or hepatotoxic risk, positioning 6,8-diprenylgenistein as a promising lead scaffold. This integrated phytochemical, biochemical and computational study uncovers T. villosa as a rich source of allosteric PTP1B inhibitors and highlights diprenylated flavonoids as tractable starting points for antidiabetic and anti-obesity drug development.