Advancing drug-lead and chemical-probe discovery using weighted-ensemble simulations and biophysical validation

项目摘要 该项目将研究La相关蛋白1（LARP 1），这是一种允许细胞快速增加的分子开关。 蛋白质合成LARP 1储存和保护制造核糖体蛋白所需的mRNA分子。在 响应促生长信号或癌症，雷帕霉素复合物1（mTORC 1）的哺乳动物靶引起 LARP 1释放其结合的mRNA。核糖体产量激增，导致蛋白质产量迅速增加 综合一般。 我们强大的初步数据使我们得出两个核心假设。首先，我们假设LARP 1- 结合分子（配体）将干扰LARP 1 mRNA储存机制，从而减少蛋白质 合成.其次，我们假设，更好地了解分子结合蛋白的灵活性， 口袋-包括LARP 1口袋-将改善合理的配体设计。我们将在两个方面来检验这些假设。 目标。Aim 1将创建一种新的以口袋为中心的方法来模拟蛋白质，称为SubPEx。我们将证明 SubPEx可以有效地揭示两个良好表征的动态口袋的灵活性（来自TEM-1 B-1）。 内酰胺酶和流感神经氨酸酶）。目标2将使用SubPEx、虚拟筛选和生物物理 实验以鉴定结合柔性LARP 1口袋的新配体。 这项工作在几个方面具有重要意义。LARP 1配体将作为基础科学工具（化学探针） 来增进我们对LARP 1生物学的理解。此外，癌症需要大量的蛋白质合成， 破坏mTORC 1-LARP 1信号传导的分子将作为进一步开发新的 治疗大多数mTORC 1通路抑制剂结合mTOR本身。它们容易发生耐药性突变 和/或不完全抑制。LARP 1抑制将提供独特和创新的药理学方法。 SubPEx本身也将产生影响。许多蛋白质药物靶标具有高度柔性的结合口袋， 成功基于结构的药物设计必须考虑这种灵活性。与其他探索方法不同， 蛋白质的灵活性，SubPEx将集中在结合口袋本身的计算工作。它的宽容，开放- 源代码许可证将鼓励采用。我们预计，更广泛的社区中的许多人也将使用SubPEx 来设计结合自身疾病相关蛋白的配体。

Project Summary This project will study La-related protein 1 (LARP1), a molecular switch that allows cells to rapidly increase protein synthesis. LARP1 stores and protects the mRNA molecules required to make ribosomal proteins. In response to pro-growth signals or cancer, the mammalian target of rapamycin complex 1 (mTORC1) causes LARP1 to release its bound mRNAs. Ribosome production surges, leading to rapid increases in protein synthesis generally. Our strong preliminary data has led us to two central hypotheses. First, we hypothesize that LARP1- binding molecules (ligands) will interfere with the LARP1 mRNA-storage mechanism, thereby reducing protein synthesis. Second, we hypothesize that better understanding the flexibility of molecule-binding protein pockets—including LARP1 pockets—will improve rational ligand design. We will test these hypotheses in two aims. Aim 1 will create a new pocket-centric method for simulating proteins, called SubPEx. We will show that SubPEx can effectively reveal the flexibility of two well-characterized dynamic pockets (from TEM-1 b- lactamase and influenza neuraminidase). Aim 2 will use SubPEx, virtual screening, and biophysical experiments to identify new ligands that bind flexible LARP1 pockets. This work is significant in several ways. LARP1 ligands will serve as basic-science tools (chemical probes) to advance our understanding of LARP1 biology. Additionally, cancer requires extensive protein synthesis, so molecules that disrupt mTORC1-LARP1 signaling will serve as leads that will further the development of new therapies. Most mTORC1-pathway inhibitors bind mTOR itself. They are subject to resistance mutations and/or incomplete inhibition. LARP1 inhibition will provide a unique and innovative pharmacological approach. SubPEx itself will also be impactful. Many protein drug targets have highly flexible binding pockets, and successful structure-based drug design must account for that flexibility. Unlike other methods for exploring protein flexibility, SubPEx will focus computational effort on the binding pocket itself. Its permissive, open- source license will encourage adoption. We expect that many in the broader community will also use SubPEx to design ligands that bind their own disease-relevant proteins of interest.