Mechanism-Based Allosteric Inhibition of PTP1B by Prenylated Flavonoids from Glycyrrhiza echinata: In Vitro Experiments and in Silico Validation

A phytochemical investigation of Glycyrrhiza echinata led to the isolation and structural characterization of twelve phenolic compounds. An in silico target fishing analysis identified protein tyrosine phosphatase 1B (PTP1B) as a potential biological target for these phytochemicals, prompting an in vitro evaluation of their PTP1B inhibitory activities. Gancaonin Q and licoflavone C exhibited notably low IC₅₀ values (1.61 ± 0.32 µM and 1.39 ± 0.33 µM, respectively), outperforming the reference inhibitor ursolic acid (IC₅₀ = 7.17 ± 0.69 µM), while norartocarpetin showed moderate activity (IC₅₀ = 42.41 ± 2.12 µM). Enzyme kinetic studies revealed that gancaonin Q and licoflavone C act as noncompetitive inhibitors of PTP1B. Subsequent in silico analyses supported these findings and provided mechanistic insights. Molecular docking confirmed robust binding interactions for gancaonin Q and licoflavone C at the PTP1B allosteric site. Free energy landscape (FEL) calculations indicated that both compounds stabilized the enzyme within low-energy conformations, and MM/PBSA estimations corroborated their favorable binding free energies. Molecular dynamics simulations further demonstrated the stability of the ligand-enzyme complexes, characterized by reduced structural fluctuations in comparison with the free enzyme and norartocarpetin-bound states. Finally, ADMET assessments indicated promising pharmacokinetic and toxicity profiles, with some scope for structural refinement. Overall, these results highlight gancaonin Q and licoflavone C as promising lead compounds for the development of PTP1B inhibitors with therapeutic potential.