Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, TX 75205, USA.
Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA.
Int J Mol Sci. 2023 May 19;24(10):9009. doi: 10.3390/ijms24109009.
The Hippo pathway is an evolutionary conserved signaling network involved in several cellular regulatory processes. Dephosphorylation and overexpression of Yes-associated proteins (YAPs) in the Hippo-off state are common in several types of solid tumors. YAP overexpression results in its nuclear translocation and interaction with transcriptional enhanced associate domain 1-4 (TEAD1-4) transcription factors. Covalent and non-covalent inhibitors have been developed to target several interaction sites between TEAD and YAP. The most targeted and effective site for these developed inhibitors is the palmitate-binding pocket in the TEAD1-4 proteins. Screening of a DNA-encoded library against the TEAD central pocket was performed experimentally to identify six new allosteric inhibitors. Inspired by the structure of the TED-347 inhibitor, chemical modification was performed on the original inhibitors by replacing secondary methyl amide with a chloromethyl ketone moiety. Various computational tools, including molecular dynamics, free energy perturbation, and Markov state model analysis, were employed to study the effect of ligand binding on the protein conformational space. Four of the six modified ligands were associated with enhanced allosteric communication between the TEAD4 and YAP1 domains indicated by the relative free energy perturbation to original molecules. Phe229, Thr332, Ile374, and Ile395 residues were revealed to be essential for the effective binding of the inhibitors.
Hippo 通路是一个进化上保守的信号网络，参与多种细胞调节过程。在 Hippo 失活状态下，Yes 相关蛋白（YAP）的去磷酸化和过表达在几种实体肿瘤中很常见。YAP 的过表达导致其核转位，并与转录增强相关域 1-4（TEAD1-4）转录因子相互作用。已经开发了共价和非共价抑制剂来针对 TEAD 和 YAP 之间的几个相互作用位点。这些开发的抑制剂最针对和有效的位点是 TEAD1-4 蛋白中的棕榈酸结合口袋。通过实验对 TEAD 中心口袋进行 DNA 编码文库筛选，以鉴定六种新的别构抑制剂。受 TED-347 抑制剂结构的启发，对原始抑制剂进行了化学修饰，用氯甲基酮取代二级甲基酰胺。使用各种计算工具，包括分子动力学、自由能扰动和 Markov 状态模型分析，研究配体结合对蛋白质构象空间的影响。在六种修饰的配体中，有四种与 TEAD4 和 YAP1 结构域之间增强的别构通讯相关，这是通过对原始分子的相对自由能扰动来表示的。揭示了 Phe229、Thr332、Ile374 和 Ile395 残基对于抑制剂的有效结合是必不可少的。
