背景:SHP2是一种非受体蛋白酪氨酸磷酸酶,可去除酪氨酸磷酸化。功能上,SHP2是连接许多致癌细胞信号级联的重要桥梁,包括RAS-ERK,PI3K-AKT,JAK-STAT,和PD-1/PD-L1通路。本研究旨在使用基于层次结构的虚拟筛选策略来发现新颖且有效的SHP2抑制剂,该策略结合了分子对接和片段分子轨道方法(FMO)来计算结合亲和力(称为Dock-FMO协议)。对于SHP2目标,FMO方法预测的蛋白质-配体相互作用的结合亲和力与实验值之间具有高度相关性(R2=0.55),证明了与MM/PBSA(R2=0.02)和MM/GBSA(R2=0.15)方法相比的显着优势。因此,我们采用Dock-FMO虚拟筛选ChemDiv数据库的~2,990,000种化合物,以鉴定一种新型的SHP2变构抑制剂,带有羟基亚氨基乙酰胺支架。实验验证表明,新化合物(E)-2-(羟基亚氨基)-2-苯基-N-(哌啶-4-基甲基)乙酰胺(7188-0011)以剂量依赖性方式有效抑制SHP2。分子动力学(MD)模拟分析揭示了化合物7188-0011与SHP2蛋白的结合稳定性,以及变构结合位点中的关键相互作用残基。总的来说,我们的工作已经确定了一种靶向SHP2的新型且有前景的变构抑制剂,为进一步优化以开发更有效的抑制剂提供了新的起点.
方法:所有分子对接研究均用于确定Maestrov10.1的潜在导联。通过使用GAMESSv2020系统在MP2/6-31G*水平下的FMO计算进一步预测潜在前导的蛋白质-配体结合亲和力。通过应用FF14SB力场,使用AmberTools18进行了MD模拟。使用VMDv1.9.3分析MD轨迹。用mmpbsa进行MM/GB(PB)SA结合自由能分析。AmberTools18的py工具。对接和MD仿真结果通过PyMOLv2.5.0可视化。
BACKGROUND: SHP2 is a non-receptor protein tyrosine phosphatase to remove tyrosine phosphorylation. Functionally, SHP2 is an essential bridge to connect numerous oncogenic cell-signaling cascades including RAS-ERK, PI3K-AKT, JAK-STAT, and PD-1/PD-L1 pathways. This study aims to discover novel and potent SHP2 inhibitors using a hierarchical structure-based virtual screening strategy that combines molecular docking and the fragment molecular orbital method (FMO) for calculating binding affinity (referred to as the Dock-FMO protocol). For the SHP2 target, the FMO method prediction has a high correlation between the binding affinity of the protein-ligand interaction and experimental values (R2 = 0.55), demonstrating a significant advantage over the MM/PBSA (R2 = 0.02) and MM/GBSA (R2 = 0.15) methods. Therefore, we employed Dock-FMO virtual screening of ChemDiv database of ∼2,990,000 compounds to identify a novel SHP2 allosteric inhibitor bearing hydroxyimino acetamide scaffold. Experimental validation demonstrated that the new compound (E)-2-(hydroxyimino)-2-phenyl-N-(piperidin-4-ylmethyl)acetamide (7188-0011) effectively inhibited SHP2 in a dose-dependent manner. Molecular dynamics (MD) simulation analysis revealed the binding stability of compound 7188-0011 and the SHP2 protein, along with the key interacting residues in the allosteric binding site. Overall, our work has identified a novel and promising allosteric inhibitor that targets SHP2, providing a new starting point for further optimization to develop more potent inhibitors.
METHODS: All the molecular docking studies were employed to identify potential leads with Maestro v10.1. The protein-ligand binding affinities of potential leads were further predicted by FMO calculations at MP2/6-31G* level using GAMESS v2020 system. MD simulations were carried out with AmberTools18 by applying the FF14SB force field. MD trajectories were analyzed using VMD v1.9.3. MM/GB(PB)SA binding free energy analysis was carried out with the mmpbsa.py tool of AmberTools18. The docking and MD simulation results were visualized through PyMOL v2.5.0.