Programmable peptide-guided protein degradation

可编程肽引导的蛋白质降解

• 批准号: 10741655
• 负责人: Pranam Chatterjee
• 金额: $ 38.77万
• 依托单位: DUKE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-09-01 至 2025-08-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10741655
• 关键词: 2019-nCoV; Active Sites; Address; Algorithms; Amino Acid Sequence; Antibodies; Architecture; Base Sequence; Binding; Biological Assay; CRISPR/Cas technology; Cells; Chemistry; Chimera organism; Chimeric Proteins; Code; Complex; Consumption; DNA; Data Set; Databases; Development; Disease; Employment; Encapsulated; Engineering; Fibronectins; Fluorescence; Formulation; Foundations; Gene Delivery; Generations; Genetic; Goals; Human; In Vitro; Laboratories; Language; Learning; Length; Libraries; Malignant Neoplasms; Masks; Mediating; Messenger RNA; Methodology; Methods; Modality; Modeling; Molecular Conformation; Mutagenesis; Output; Pathogenicity; Peptides; Phosphoric Monoester Hydrolases; Phosphotransferases; Positioning Attribute; Post-Translational Protein Processing; Protac; Protein Engineering; Protein Isoforms; Proteins; Proteome; Protocols documentation; RNA; Rapid screening; Research; Specific qualifier value; Structure; Techniques; Technology; Testing; Therapeutic; Training; Translating; Translations; Ubiquitin-Proteasomal Pathway; Validation; Variant; Work; design; disease phenotype; experimental analysis; gene therapy; grasp; in silico; in vivo; in vivo evaluation; interest; iterative design; lipid nanoparticle; mutant; nanobodies; novel therapeutic intervention; novel therapeutics; pharmacologic; protein aminoacid sequence; protein complex; protein degradation; protein protein interaction; rapid testing; scaffold; screening; small molecule; small molecule inhibitor; tool; ubiquitin-protein ligase

Summary Over 600 human proteins have been recently prioritized as key cancer targets, with nearly half being considered ‘intractable’ by standard small-molecule inhibition approaches, due to target instability and active site accessibility constraints. By redirecting the ubiquitin-proteasomal pathway (UPS) for targeted protein degradation, the proteolysis-targeting chimera (PROTAC) technology provides a potential solution, enabling rapid and continuous target consumption as well as the stronger pharmacological effects than small molecule inhibition. Nonetheless, PROTACs suffer from similar developmental hurdles as small molecules and cannot be easily designed for motif or post-translational modification-specific targeting. To address these hurdles, research efforts have shifted toward gene therapy approaches by introducing the concept of protein-mediated protein degradation. Here, E3 ubiquitin ligases are redirected by replacing their natural substrate binding domains with “off-the-shelf” binding domains, including nanobodies, antibodies, and DARPins, to generate target-specific ubiquibodies. To augment this platform, we recently exploited natural protein-protein interaction information to develop algorithmic pipelines that prioritize target-selective peptides which can be fused to the E3 ubiquitin ligase conjugation domains to induce target protein degradation. In this project, we will augment our current methods to enable the development of these ubiquibodies (uAbs) for any protein, including those deemed ‘intractable’ by small molecule-based means. To do this, we will automate a bipartite algorithmic pipeline that leverages recent advancements in protein language modeling as well as existing co-complex databases to design peptide binders to diverse protein targets, including those with solved co-crystals as well as those with minimal structural information. Specifically, our pipeline will take user-specified target proteins as inputs, and generate prioritized lists of candidate peptide binders as outputs, enabling subsequent generation of uAbs for target degradation. Through library-on-library fluorescence-based assays in human cells and subsequent encapsulation of uAb mRNA in lipid nanoparticles (LNPs), we will develop a scalable method to test and translate our degraders for downstream in vivo validation. In total, this work will generate a robust peptide design tool that will enhance targeted protein degradation efforts and lay the foundation for programmable proteome editing.

概括 最近，超过 600 种人类蛋白质被优先列为关键癌症靶标，其中近一半是 由于目标不稳定性和活性，标准小分子抑制方法被认为是“棘手的” 通过重定向目标蛋白的泛素-蛋白酶体途径（UPS）。 降解，蛋白水解靶向嵌合体（PROTAC）技术提供了一个潜在的解决方案，使 快速持续的靶向消耗以及比小分子更强的药理作用 然而，PROTAC 也面临着与小分子类似的发展障碍，并且不能被抑制。 轻松设计用于特定主题或翻译后修饰的靶向。 通过引入蛋白质介导的概念，研究已转向基因治疗方法 此处，E3 泛素连接酶通过替换其天然底物结合而被重定向。 具有“现成”结合域的域，包括纳米抗体、抗体和 DARPins，以生成 为了增强这个平台，我们最近利用了天然的蛋白质-蛋白质相互作用。 信息来开发优先考虑目标选择性肽的算法管道，这些肽可以融合到 E3 泛素连接酶缀合域可诱导靶蛋白降解 在本项目中，我们将增强。 我们目前的方法能够为任何蛋白质开发这些泛在体 (uAb)，包括那些 基于小分子的方法被认为是“棘手的”，为此，我们将自动化二分算法。 利用蛋白质语言建模的最新进展以及现有的复合体的管道 用于设计针对不同蛋白质靶点的肽结合剂的数据库，包括那些具有已解决的共晶的蛋白质结合剂 具体来说，我们的管道将采用用户指定的目标蛋白质作为那些具有最少结构信息的蛋白质。 输入，并生成候选肽结合物的优先列表作为输出，从而实现后续生成 通过在人体细胞中进行基于库上库的荧光测定，对 uAb 进行靶点降解。 随后将 uAb mRNA 封装在脂质纳米颗粒 (LNP) 中，我们将开发一种可扩展的方法 测试并翻译我们的降解剂以进行下游体内验证。总的来说，这项工作将产生强大的结果。 肽设计工具将增强靶向蛋白质降解工作并为 可编程蛋白质组编辑。