Structure-based discovery and conformational analysis of non-phosphomimetic bidentate inhibitor for protein tyrosine phosphatase 1B

Abstract

Protein tyrosine phosphatase 1B (PTP1B) is a key regulator of glucose homeostasis and signaling pathways, making it an attractive therapeutic target for type 2 diabetes, obesity, and cancer. However, conventional phosphomimetic inhibitors suffer from poor bioavailability and selectivity due to the flat, positively charged, and solvent-exposed nature of the PTP1B active site. To address these limitations, we employed a structure-based molecular modeling approach—combining high-throughput virtual screening, molecular dynamics, UMAP analysis, and JS divergence—to investigate novel non-phosphomimetic bidentate inhibitors. Among the identified candidates, COM68 and COM63 exhibited stable binding modes with favorable binding free energies. However, UMAP-based structural quantification revealed that COM63 displayed higher residue fluctuations at key binding sites, particularly R24 and F182. Subsequent in vitro assays confirmed that COM63 was inactive at the tested concentrations, suggesting that these excess fluctuations hindered effective PTP1B inhibition. In contrast, COM68 demonstrated an IC50 of 72 μM, indicating its potential as a lead compound for further optimization. Furthermore, ADMET predictions of COM68 indicated favorable pharmacokinetic properties, supporting its suitability for future drug development. This study identified a novel non-phosphomimetic bidentate inhibitor and highlighted the importance of stabilizing interactions at key residues in PTP1B inhibitor design. These findings provide structural insights for developing more selective and effective PTP1B inhibitors. © 2025 The Authors