Coiled-coil Technology for Regulating Intracellular Protein-protein Interactions

用于调节细胞内蛋白质-蛋白质相互作用的卷曲螺旋技术

• 批准号: BB/V008412/1
• 负责人: Andrew Wilson
• 金额: $ 60.45万
• 依托单位: University of Leeds
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2021
• 资助国家: 英国
• 起止时间: 2021 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FV008412%2F1
• 关键词: Coiled; coil; Technology; Regulating; Intracellular

Proteins are the workhorses of biology. Proteins rarely work alone, and they cooperative via so called protein-protein interactions. In this way, they form larger assemblies and networks of proteins. In turn, these provide frameworks for controlling all cellular processes that regulate life. Dysregulation of the underlying protein-protein interactions can result in disease. The scale of this framework of protein-protein interactions within a cell is enormous; it has been estimated to be around 650,000 different interactions. These present considerable opportunities for intervening in biological processes (a) to understand healthy cells better, and (b) to develop new therapeutics when subcellular mechanisms go wrong. There are different ways to do this. We propose a new approach that employs synthetic protein modules (i) to disrupt protein-protein interactions and (ii) to hijack endogenous cell machineries. Synthetic chemical probes-such as small-molecule drugs-function by binding to a protein target within the body. This can be used to interfere with the target protein's function to help understand its biological role and as a starting point for drug discovery. Most chemical probes bind to well-defined pockets in proteins; this is analogous to a key fitting into a lock. By contrast, the design of probes to interfere with protein-protein interactions generally requires a fundamentally different type of association between the probe and one of the interacting target proteins; analogous to a hand gripping a ball. Thus, the development of effective probes that target protein-protein interactions raises new challenges that need to be met in future chemical biology and drug discovery. Two emerging approaches are promising for this, and we propose to combine them in this grant application.The first is a synthetic-biology approach. This uses synthetic proteins called de novo coiled coils as scaffolds for building new protein-protein interactions from scratch. This is attractive because natural coiled-coil proteins exhibit an array of protein-recognition properties and we can design de novo coiled-coils with diverse structures thereby expanding their potential. The second involves the targeted destruction of cellular proteins; in essence, this is a search-and-destroy strategy that co-opts the cell's own waste-disposal machineries so as to block protein function or remove harmful proteins that cause disease. The proposed research will develop new methodologies (i) to disrupt specified protein-protein interactions and (ii) to target certain proteins of interest for degradation. In this way, we will regulate specified processes in cells. To do this, we will not use conventional small molecules as the probes for intervening in the underlying protein-protein interactions. Rather, we will employ the synthetic coiled coils and adapt these to recognise the target proteins. In addition, for the second application, the coiled coils will be modified further to link the target protein to the cell's degradation pathways. Our aim is to deliver methods and reagents that will be of use to others in studying biological function and for developing new drugs to treat disease.This work is necessarily interdisciplinary. Therefore, we bring together a team of computational and experimental chemists, biochemists and cell biologists to tackle it, and we partner with a biotech company to translate the work in timely and relevant manner.

蛋白质是生物学的主力。蛋白质很少单独工作，它们通过所谓的蛋白质-蛋白质相互作用进行合作。通过这种方式，它们形成更大的蛋白质组装体和网络。反过来，它们提供了控制所有调节生命的细胞过程的框架。潜在的蛋白质-蛋白质相互作用的失调可能导致疾病。细胞内蛋白质-蛋白质相互作用的框架规模是巨大的。据估计，大约有 650,000 种不同的互动。这些为干预生物过程提供了相当多的机会（a）更好地了解健康细胞，以及（b）当亚细胞机制出现问题时开发新的疗法。有不同的方法可以做到这一点。我们提出了一种新方法，采用合成蛋白质模块（i）破坏蛋白质-蛋白质相互作用和（ii）劫持内源细胞机器。合成化学探针（例如小分子药物）通过与体内的蛋白质靶标结合而发挥作用。这可用于干扰靶蛋白的功能，以帮助了解其生物学作用并作为药物发现的起点。大多数化学探针与蛋白质中明确的口袋结合。这类似于一把钥匙插入一把锁。相比之下，干扰蛋白质-蛋白质相互作用的探针设计通常需要探针与相互作用的靶蛋白之一之间存在根本不同类型的关联。类似于一只手握住球。因此，开发针对蛋白质-蛋白质相互作用的有效探针提出了未来化学生物学和药物发现中需要应对的新挑战。两种新兴方法对此很有希望，我们建议在本次拨款申请中将它们结合起来。第一种是合成生物学方法。它使用称为“从头卷曲线圈”的合成蛋白质作为支架，从头开始构建新的蛋白质-蛋白质相互作用。这很有吸引力，因为天然卷曲螺旋蛋白表现出一系列蛋白质识别特性，我们可以从头设计具有不同结构的卷曲螺旋，从而扩展其潜力。第二个涉及有针对性地破坏细胞蛋白质；从本质上讲，这是一种搜索和破坏策略，利用细胞自身的废物处理机制来阻止蛋白质功能或去除导致疾病的有害蛋白质。 拟议的研究将开发新的方法（i）破坏特定的蛋白质-蛋白质相互作用和（ii）针对某些感兴趣的蛋白质进行降解。通过这种方式，我们将调节细胞内的特定过程。为此，我们不会使用传统的小分子作为干预潜在蛋白质-蛋白质相互作用的探针。相反，我们将使用合成的卷曲线圈并对其进行调整以识别目标蛋白质。此外，对于第二个应用，卷曲线圈将被进一步修改，以将目标蛋白与细胞的降解途径连接起来。我们的目标是提供可用于其他人研究生物功能和开发治疗疾病的新药的方法和试剂。这项工作必然是跨学科的。因此，我们召集了一个由计算和实验化学家、生物化学家和细胞生物学家组成的团队来解决这个问题，并与一家生物技术公司合作，及时、相关地转化这项工作。

项目成果

Peptide Macrocyclization via Intramolecular Interception of Visible-Light-Mediated Desulfurization

通过分子内拦截可见光介导的脱硫进行肽大环化

• DOI: http://dx.10.26434/chemrxiv-2023-865v6-v2
• 发表时间: 2023
• 作者: Smith F

Maleimide constrained BAD BH3 domain peptides as BCL-xL Inhibitors: A versatile approach to rapidly identify sites compatible with peptide constraining

作为 BCL-xL 抑制剂的马来酰亚胺约束 BAD BH3 结构域肽：快速识别与肽约束兼容的位点的通用方法

• DOI: http://dx.10.1016/j.bmcl.2023.129260
• 发表时间: 2023
• 期刊: Bioorganic & Medicinal Chemistry Letters
• 影响因子: 2.7
• 作者: Zhang P

Peptide Macrocyclization via Intramolecular Interception of Visible-Light-Mediated Desulfurization

通过分子内拦截可见光介导的脱硫进行肽大环化

• DOI: http://dx.10.26434/chemrxiv-2023-865v6
• 发表时间: 2023
• 作者: Smith F

Rational design of Harakiri (HRK)-derived constrained peptides as BCL-xL inhibitors.

Harakiri (HRK) 衍生的限制肽作为 BCL-xL 抑制剂的合理设计。

• DOI: http://dx.10.1039/d2cc06029a
• 发表时间: 2023
• 期刊: Chemical communications (Cambridge, England)
• 作者: Zhang P