Elucidation of a structural rationale for the binding of Myc by small molecule inhibitors

阐明小分子抑制剂结合 Myc 的结构原理

• 批准号: 10398915
• 负责人: Mihai Ioan Truica
• 金额: $ 4.56万
• 依托单位: NORTHWESTERN UNIVERSITY AT CHICAGO
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-05-01 至 2024-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10398915
• 关键词: Address; Affinity; Amino Acid Sequence; Amino Acids; Anabolism; Behavior; Binding; Binding Proteins; Biological Assay; Biophysics; C-terminal; Cell physiology; Cells; Clinical; Co-Immunoprecipitations; Code; Coupled; Crystallization; Data; Degradation Pathway; Development; Disease; Drug Design; Drug Kinetics; Ensure; Entropy; Event; Free Energy; Goals; Hot Spot; Human; Hydrophobicity; In Vitro; Interferometry; Knowledge; MYC Family Protein; MYC gene; Malignant - descriptor; Malignant Neoplasms; Medical Research; Metabolism; Molecular; Molecular Conformation; Oncogenes; Phosphorylation; Phosphotransferases; Population; Proteins; Recombinant Proteins; Research; Role; Site-Directed Mutagenesis; Specificity; Spectrum Analysis; Stretching; Structure; Surface; Surface Plasmon Resonance; System; Testing; Therapeutic; Time; Work; base; biophysical properties; cancer type; cell transformation; driving force; drug discovery; experimental study; flexibility; glycogen synthase kinase 3 beta; inhibitor; member; mutant; preclinical study; protein degradation; protein folding; research and development; screening; small molecule; small molecule inhibitor; theories; three dimensional structure; transcription factor; virtual

Project Summary Myc is a transcription factor essential for vital cellular processes such as proliferation, differentiation, metabolism and biosynthesis. As a result, it is often coopted during malignant transformation of cells and deregulated Myc expression occurs in virtually all cancer types. Given this role as a prominent oncogene, Myc is widely regarded as a high value cancer target. However, direct inhibition of Myc has been unsuccessful despite decades of research and development efforts. Myc is an intrinsically disordered protein (IDP) and therefore it lacks a unique, defined three-dimensional structure, which has made it extremely difficult to identify small molecule inhibitors based on traditional structure-based drug design paradigms. Instead, the protein has conformational flexibility and can access a large variety of different structures, which explains how it can recognize and bind a diverse assortment of protein partners dependent on cellular context. Notwithstanding the lack of any defined pockets in the Myc protein, several groups have identified small molecules that can disrupt Myc function. However, none of these inhibitors have made it to rigorous preclinical studies due to poor pharmacokinetic profiles and weak potency. Furthermore, there have been little to no studies demonstrating target engagement by small molecule probes of Myc in cells. This work is addressing these key barriers to progress. Small molecule binding to intrinsically disordered proteins is governed by different biophysical driving forces compared to binding of small molecules to globular, folded proteins. Binding to IDPs causes a shift in the population of available conformations and the resulting increase in entropy is the main driver of the free energy of binding. However, binding events only occur within regions on IDPs which are less disordered and more hydrophobic, providing for key, despite being relatively weak, enthalpic interactions that ensure specificity of binding. I hypothesize that Myc possesses a sequence of amino acids that serves as a small molecule binding hotspot. Using a panel of Myc mutant constructs, coupled with biotinylated small molecule Myc binders, I will elucidate the role of this Myc binding hotspot in small molecule recognition. I also hypothesize that a shift in conformational space occurs as a result of binding this Myc hotspot which directly results in an increased rate of Myc protein degradation. My preliminary data suggests that small molecule binding of Myc promotes increased interaction with proteins involved in the Myc phosphorylation and degradation pathway. Therefore, I will also elucidate how binding impacts Myc protein degradation. These experiments will advance our understanding of the factors that promote binding to IDPs and how we can leverage them to progress towards the ultimate goal of identifying a suitable clinical small molecule Myc inhibitor.

项目摘要 MYC是一种转录因子，对重要的细胞过程如增殖、分化、新陈代谢是必不可少的 和生物合成。因此，在细胞恶性转化和去调控的Myc过程中，它经常被增选。 几乎在所有类型的癌症中都有表达。鉴于这一重要癌基因的作用，Myc被广泛认为 作为高价值的癌症靶点。然而，尽管几十年来对Myc的直接抑制一直没有成功 研究和开发的努力。MYC是一种固有的无序蛋白质(IDP)，因此它缺乏一种独特的， 明确的三维结构，这使得识别小分子抑制剂变得极其困难 基于传统的基于结构的药物设计范式。相反，这种蛋白质具有构象灵活性。 并可以访问大量不同的结构，这解释了它如何识别和绑定不同的 蛋白质伴侣的分类取决于细胞环境。尽管没有任何定义的口袋在 Myc蛋白，几个研究小组已经发现了可以破坏Myc功能的小分子。然而，没有一个 这些抑制剂已经进入了严格的临床前研究，因为它们的药代动力学曲线不佳，而且 威力。此外，很少或根本没有研究表明小分子参与靶标作用。 细胞内Myc的探针。这项工作正在解决这些阻碍进展的关键障碍。 与固有无序蛋白质结合的小分子受不同生物物理驱动力的支配 与小分子与球状折叠蛋白质的结合相比。与国内流离失所者的绑定导致了 可用构象的布居和由此导致的熵的增加是自由能的主要驱动力 是有约束力的。然而，绑定事件只发生在国内流离失所者上的区域内，这些区域较少无序，更多 疏水性，提供关键的，尽管是相对较弱的，焓相互作用，确保特异性 有约束力的。我假设Myc有一个氨基酸序列，作为一个小分子 绑定热点。使用一组Myc突变构建体，再加上生物素化的小分子Myc结合剂， 我将阐明这个Myc结合热点在小分子识别中的作用。我还假设，一种转变 由于结合了这个Myc热点而发生在构象空间中，这直接导致了 Myc蛋白降解率增加。我的初步数据表明，Myc的小分子结合 促进与参与Myc磷酸化和降解途径的蛋白质增加相互作用。 因此，我还将阐明结合如何影响Myc蛋白的降解。这些实验将会取得进展 我们对促进约束国内流离失所者的因素的理解，以及我们如何利用这些因素来取得进展 最终目标是找到一种合适的临床小分子Myc抑制剂。