Screening and identification of potential PTP1B allosteric inhibitors using <i>in silico</i> and <i>in vitro</i> approaches

Protein tyrosine phosphatase 1B (PTP1B) is a validated therapeutic target for Type 2 diabetes due to its specific role as a negative regulator of insulin signaling pathways. Discovery of active site directed PTP1B inhibitors is very challenging due to highly conserved nature of the active site and multiple charge requirements of the ligands, which makes them non-selective and non-permeable. Identification of the PTP1B allosteric site has opened up new avenues for discovering potent and selective ligands for therapeutic intervention. Interactions made by potent allosteric inhibitor in the presence of PTP1B were studied using Molecular Dynamics (MD). Computationally optimized models were used to build separate pharmacophore models of PTP1B and TCPTP, respectively. Based on the nature of interactions the target residues offered, a receptor based pharmacophore was developed. The pharmacophore considering conformational flexibility of the residues was used for the development of pharmacophore hypothesis to identify potentially active inhibitors by screening large compound databases. Two pharmacophore were successively used in the virtual screening protocol to identify potential selective and permeable inhibitors of PTP1B. Allosteric inhibition mechanism of these molecules was established using molecular docking and MD methods. The geometrical criteria values confirmed their ability to stabilize PTP1B in an open conformation. 23 molecules that were identified as potential inhibitors were screened for PTP1B inhibitory activity. After screening, 10 molecules which have good permeability values were identified as potential inhibitors of PTP1B. This study confirms that selective and permeable inhibitors can be identified by targeting allosteric site of PTP1B.蛋白酪氨酸磷酸酶1B（Protein tyrosine phosphatase 1B, PTP1B）是经过验证的2型糖尿病治疗靶点，因其作为胰岛素信号通路负调控因子发挥特异性作用。由于活性位点高度保守且配体需满足多重电荷要求，导致其选择性差、膜通透性不佳，靶向活性位点的PTP1B抑制剂研发极具挑战性。PTP1B变构位点的发现为开发强效且选择性的治疗用配体开辟了新途径。研究人员借助分子动力学（Molecular Dynamics, MD）技术，分析了PTP1B与强效变构抑制剂结合后的相互作用模式。通过计算优化模型分别构建了PTP1B及T细胞蛋白酪氨酸磷酸酶（TCPTP）的药效团模型；基于靶标残基的相互作用特性，开发了基于受体的药效团模型。考虑残基构象灵活性的药效团被用于构建药效团假说，以通过大规模化合物数据库筛选识别潜在活性抑制剂。研究先后采用两个药效团模型开展虚拟筛选流程，以筛选得到PTP1B的选择性及膜通透性良好的潜在抑制剂。借助分子对接与分子动力学方法，阐明了这类分子的变构抑制机制。几何参数验证了它们可稳定PTP1B的开放构象。研究人员对23个经初步筛选得到的潜在抑制剂分子开展了PTP1B抑制活性检测，最终筛选得到10个具备良好膜通透性的PTP1B潜在抑制剂。本研究证实，通过靶向PTP1B的变构位点，可开发得到兼具选择性与膜通透性的PTP1B抑制剂。