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: 10216159
• 负责人: Mihai Ioan Truica
• 金额: $ 4.22万
• 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/10216159
• 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/antagonist; 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是一种重要的转录因子，参与细胞的增殖、分化、代谢等过程 和生物合成。因此，在细胞恶性转化和Myc失调控过程中， 几乎在所有类型的癌症中都有表达。鉴于Myc作为一个重要的致癌基因的作用， 作为高价值的癌症靶点。然而，直接抑制Myc一直是不成功的，尽管几十年来， 研究和开发工作。Myc是一种内在无序蛋白（IDP），因此它缺乏一个独特的， 定义的三维结构，这使得识别小分子抑制剂变得非常困难 基于传统的基于结构的药物设计范例。相反，该蛋白质具有构象灵活性 并且可以访问各种不同的结构，这解释了它如何识别和结合各种各样的 蛋白质伴侣的分类取决于细胞环境。尽管缺乏任何明确的口袋里， Myc蛋白，几个研究小组已经鉴定出可以破坏Myc功能的小分子。但是没有一 这些抑制剂由于药代动力学特性差和弱的 力量此外，几乎没有研究表明小分子的靶向接合， Myc在细胞中的作用这项工作正在解决这些阻碍进展的关键障碍。 小分子与内在无序蛋白质的结合受不同的生物物理驱动力控制 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结合导致 可用构象的数量和由此产生的熵的增加是自由能的主要驱动力 的约束。然而，结合事件仅发生在IDP上的区域内，这些区域较不无序且较不稳定。 疏水的，提供关键的，尽管是相对弱的，疏水的相互作用，确保特异性， 约束力我假设Myc拥有一个氨基酸序列， 结合热点使用一组Myc突变体构建体，与生物素化的小分子Myc结合剂偶联， 我将阐明这种Myc结合热点在小分子识别中的作用。我还假设 在构象空间中，由于结合该Myc热点而发生，其直接导致 Myc蛋白降解速率增加。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的相互作用增加。 因此，我也将阐明结合如何影响Myc蛋白降解。这些实验将推进 我们对促进与境内流离失所者联系的因素的理解，以及我们如何利用这些因素， 最终目标是鉴定合适的临床小分子Myc抑制剂。