Rational PROTAC design enabled by integrated in silico molecular modeling and in vitro biomimetic affinity assessment

通过集成计算机分子建模和体外仿生亲和力评估实现合理的 PROTAC 设计

• 批准号: 10728205
• 负责人: QUAN JASON CHENG
• 金额: $ 22.67万
• 依托单位: UNIVERSITY OF CALIFORNIA RIVERSIDE
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-08-01 至 2025-07-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10728205
• 关键词: Affect; Affinity; Attention; Back; Binding; Binding Proteins; Biological Assay; Biomedical Research; Biomimetics; Biophysics; Cell membrane; Cells; Complex; Computer Models; Disease; Dose; Drug Targeting; Drug resistance; Environment; Excision; Goals; In Vitro; Investigation; Knowledge; Label; Left; Ligands; Lipids; Lysosomes; Malignant Neoplasms; Measurement; Membrane; Membrane Lipids; Methodology; Modality; Modeling; Molecular; Mutagenesis; Property; Protac; Protein Dynamics; Proteins; Receptor Protein-Tyrosine Kinases; Reporting; Research; Role; Structure; Structure-Activity Relationship; Surface Plasmon Resonance; System; Technology; Theoretical model; Therapeutic; Thinness; Ubiquitination; Work; anaplastic lymphoma kinase; design; drug candidate; drug development; experience; experimental study; fabrication; in silico; in vitro Assay; inhibitor; innovation; insight; interest; molecular modeling; molecular recognition; multicatalytic endopeptidase complex; novel drug class; protein degradation; screening; side effect; small molecule; stem; ubiquitin-protein ligase

Rational PROTAC design enabled by integrated in silico molecular modeling and in vitro biomimetic affinity assessment Proteolysis targeting chimeras, or PROTACs, have received considerable attention in recent years as a new class of drugs as compared to traditional inhibitors. These small molecules target selective degradation of proteins of interest utilizing cell’s native protein degradation machinery including proteosomes and lysosomes. The benefits of PROTACs stem from an entirely different paradigm of protein targeting, which provides a unique path to target previously “undruggable” proteins and allows for smaller doses and thus lower side-effects. However, the complex mechanism of action has left a large knowledge gap towards the understanding of molecular interactions in different stages, especially on factors that control and stabilize the ternary complex that leads to ubiquitination and removal. In addition, existing technology lacks of strategies to model and confirm the linker region of the PROTAC for their roles in affecting the affinities of the warheads and contributing to the stability of the complex. There has been no report that includes the dynamic membrane in molecular recognition modeling. A new technical platform that can identify key parameters that impact formation of stable ternary complex and has the capability of screening molecular interactions with detailed information on structural insights is highly desired. To fill the unmet need, we propose to develop a collaborative work plan via a combination of in silico modeling and in vitro surface plasmon resonance (SPR)-based affinity assessment. We aim to identify features that lead to formation of stable ternary complexes for efficient PROTAC design. To establish and prove the technical feasibility, we will study anaplastic lymphoma kinase (ALK), a transmembrane receptor tyrosine kinase that is an important drug target for a variety of cancers, and an E3 ligase CRBN which has been used to promote protein degradation. Specifically, we propose three aims: Aim 1. Establish a molecular modeling platform for rational PROTAC design. The platform incorporates protein dynamics and inputs from experiments and can adapt various experimental settings such as membrane environment used in SPR. Aim 2. Build and characterize modeled PROTACs and biomimetic membranes. This includes generating PROTAC-compatible membrane mimics and structural characterization of the interfaces for membrane-bound proteins for SPR analysis. Aim 3. Investigate interaction properties of PROTAC candidates’ in biomimetic membranes. This includes on-line in vitro experiments and screening for the PROTACs at stabilizing the ternary complexes. The identification of stable PROTAC complexes will be used into further exploration into the understanding of the structure-function relationship of the system.

通过集成硅分子模型和体外技术实现合理的 PROTAC 设计 仿生亲和力评估 靶向嵌合体（PROTAC）的蛋白水解近年来受到了相当多的关注，因为 与传统抑制剂相比，这些小分子是一类新型药物，其目标是选择性降解。 利用细胞的天然蛋白质降解机制（包括蛋白酶体和 PROTAC 的优势源于一种完全不同的蛋白质靶向范式， 提供了一种独特的途径来靶向以前“不可成药”的蛋白质，并允许更小的剂量，从而 然而，其复杂的作用机制给人们留下了巨大的知识空白。 了解不同阶段的分子相互作用，特别是控制和稳定分子相互作用的因素 此外，现有技术缺乏策略。 建模并确认 PROTAC 的连接区域在影响弹头亲和力方面的作用 并有助于复合物的稳定性 目前还没有包括动态膜的报道。 分子识别建模中的新技术平台，可以识别影响的关键参数。 形成稳定的三元复合物，并具有筛选分子相互作用的能力 非常需要有关结构见解的信息。 为了满足未满足的需求，我们建议通过计算机模拟的组合来制定协作工作计划 我们的目标是通过建模和基于体外表面等离子共振（SPR）的亲和力评估来确定。 这些特性可形成稳定的三元复合物，从而实现高效的 PROTAC 设计。 为了证明技术可行性，我们将研究间变性淋巴瘤激酶（ALK），一种跨膜受体 酪氨酸激酶是多种癌症的重要药物靶点，E3 连接酶 CRBN 具有 具体来说，我们提出了三个目标： 目标 1. 建立一个分子。 用于合理 PROTAC 设计的建模平台 该平台结合了蛋白质动力学和输入。 实验并可以适应各种实验设置，例如 Aim 中使用的膜环境。 2. 构建并表征模型 PROTAC 和仿生膜 这包括生成。 PROTAC 兼容的膜模拟和膜结合界面的结构表征 目标 3. 研究 PROTAC 候选蛋白在仿生中的相互作用特性。 这包括在线体外实验和筛选 PROTAC 来稳定膜。 三元配合物的鉴定将用于进一步探索。 理解系统的结构-功能关系。