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(LARP1)，这是一种允许细胞迅速增加的分子开关 蛋白质合成。LARP1存储和保护制造核糖体蛋白所需的mRNA分子。在……里面 对促生长信号或癌症的反应，雷帕霉素复合体1(MTORC1)的哺乳动物靶标导致 LARP1释放其结合的mRNAs。核糖体生产激增，导致蛋白质快速增加 一般说来，合成。 我们强劲的初步数据让我们得出了两个核心假设。首先，我们假设LARP1- 结合分子(配体)会干扰LARP1的mRNA存储机制，从而减少蛋白质 综合。第二，我们假设更好地理解分子结合蛋白的灵活性 口袋--包括LARP1口袋--将改进有理配体的设计。我们将分两个阶段检验这些假说 目标。AIM 1将创造一种新的以口袋为中心的蛋白质模拟方法，称为SubPEx。我们将证明这一点 SubPEx可以有效地揭示两个特征良好的动态口袋的灵活性(来自TEM-1b- 内酰胺酶和流感神经氨酸酶)。AIM 2将使用SubPEx、虚拟筛选和生物物理 识别结合灵活的LARP1口袋的新配体的实验。 这项工作在几个方面具有重要意义。LARP1配体将作为基础科学工具(化学探测器) 以促进我们对LARP1生物学的理解。此外，癌症需要广泛的蛋白质合成，所以 干扰mTORC1-LARP1信号转导的分子将作为先导，进一步发展新的 治疗。大多数mTORC1途径抑制物结合mTOR本身。它们会发生抗药性突变 和/或不完全抑制。LARP1的抑制将提供一种独特的创新的药理学方法。 SubPEx本身也将产生影响。许多蛋白质药物靶标具有高度灵活的绑定口袋，并且 成功的基于结构的药物设计必须考虑到这种灵活性。与其他探索方法不同 蛋白质的灵活性，SubPEx将集中计算工作在结合口袋本身。它的宽容，开放- 源代码许可将鼓励采用。我们预计，更广泛的社区中的许多人也将使用SubPEx 设计与自身疾病相关的感兴趣蛋白结合的配体。

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.