Small molecule inhibitors and degraders of picornavirus 2A proteases as direct-acting antivirals

小核糖核酸病毒 2A 蛋白酶的小分子抑制剂和降解剂作为直接抗病毒药物

基本信息

批准号：
10514272
负责人：
Priscilla Li-ning Yang
金额：
$ 372.88万
依托单位：
STANFORD UNIVERSITY
依托单位国家：
美国
项目类别：
财政年份：
2022
资助国家：
美国
起止时间：
2022-05-16 至 2025-04-30
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10514272
关键词：
2019-nCoV Active Sites Affinity Antiviral Agents Area Binding Binding Sites Biochemistry Biological Assay Biology Cells Characteristics Chemicals Collaborations Coupling Cryoelectron Microscopy DNA DNA Sequence Alteration Data Development Dissociation Drug resistance Enterovirus Enterovirus 68 Evaluation Event FDA approved Family Picornaviridae Foundations Hepatitis C virus In Vitro Intention Lead Libraries Ligands Maps Mediating Mediator of activation protein Methods Modality Mutation Outpatients Peptide Hydrolases Pharmaceutical Chemistry Pharmaceutical Preparations Pharmacology Point Mutation Polyproteins Predisposition Proteins RNA Viruses Recombinants Recurrence Resistance Resistance profile Sampling Series Site Testing Translations Validation Variant Viral Viral Drug Resistance Viral Proteins Virus Replication Work anti-viral efficacy antiviral drug development base cytotoxicity drug development drug discovery high throughput screening inhibitor innovation interest mutant novel pandemic disease prevent protein degradation protein function protein protein interaction recruit screening small molecule small molecule inhibitor structural biology ubiquitin-protein ligase virology

项目摘要

ABSTRACT – Project 2: Small molecule inhibitors and degraders of picornavirus 2A proteases Traditional direct-acting antivirals (DAAs) target a viral protein by occupying an enzymatic pocket; dissociation of the drug leads to immediate regain of function. Consequently, most antivirals must have high-affinity, stoichiometric binding to be effective, and point mutations that reduce affinity can rapidly give rise to antiviral resistance. The established method to prevent resistance is the use of combinations of direct-acting antivirals that act via independent targets and mechanisms. In this project, we will pursue two innovative approaches to develop DAAs targeting the enterovirus (EV) 2A protease, a viral protein with at least two essential functions: (1) it catalyzes a required cleavage of the viral polyprotein and (2) it mediates a protein-protein interaction that is essential for replication. First, we will pursue targeted protein degradation (TPD) against 2A as an antiviral strategy. TPD is a new paradigm in drug development in which a small molecule that binds the target of interest is conjugated to an E3 ligase ligand resulting in protein degradation. This approach allows a wider range of protein targets because its event-driven pharmacology does not require stoichiometric inhibition of the viral protein and because the affinity required for effective protein degradation is generally lower. We previously developed the first small molecule antiviral degrader by coupling telaprevir, an FDA-approved inhibitor of the hepatitis C virus NS3-4A protease, to a ligand of the CRBNCRL E3 ubiquitin ligase. The resulting NS3 degraders inhibit HCV in vitro, including point mutants that are known to be telaprevir-resistant. Since telaprevir was recently shown to have broad-spectrum activity against enterovirus 2A proteins, we will build upon our prior work to develop telaprevir-based degraders of 2A that remove the protein from the cell and ablate all of 2A’s functions. Second, we will perform high-throughput screens for DAAs that bind to 2A and inhibit its function as a mediator of essential protein-protein interactions. Compounds discovered in these screens will be validated as 2A ligands and tested for antiviral activity, with validated ligands advanced as leads for degrader development and compounds with antiviral activity advanced as lead compounds for development of DAAs. We will also undertake screening of DNA-encoded libraries to more broadly sample chemical space and to discover additional chemical matter suitable for inhibitor and degrader development. We will also determine if DAAs targeting the active site (Aim 1) and the 2A interacting site (Aim 2) can be combined for superior efficacy and resistance profile. This work leverages the innovative discoveries made by our labs in the areas of TPD and 2A biology along with the collective expertise of our groups and the AViDD in virology, medicinal chemistry, chemical biology biochemistry, structural biology, and drug discovery. Our work developing DAAs targeting the multifunctional EV 2A protease will have wide-reaching impact by validating two new antiviral mechanisms for targeting 2A and by demonstrating the utility of TPD as an antiviral strategy.

摘要 – 项目 2：小核糖核酸病毒 2A 蛋白酶的小分子抑制剂和降解剂传统的直接作用抗病毒药物（DAA）通过占据酶解袋来靶向病毒蛋白；经过测试，药物的作用会立即恢复功能，大多数抗病毒药物必须具有高亲和力，化学计量结合是有效的，降低亲和力的点突变可以迅速产生抗病毒作用预防耐药性的既定方法是使用直接作用的抗病毒药物的组合。通过独立的目标和机制采取行动在这个项目中，我们将采取两种创新方法。开发针对肠道病毒 (EV) 2A 蛋白酶的 DAA，这是一种至少具有两个基本功能的病毒蛋白：(1) 它催化病毒多蛋白所需的裂解，并且（2）它介导蛋白质-蛋白质相互作用，即首先，我们将针对 2A 进行靶向蛋白降解（TPD）作为抗病毒药物。 TPD 策略是药物开发的新范式，其中小分子结合感兴趣的靶点。与 E3 连接酶配体缀合，导致蛋白质降解。这种方法允许更广泛的降解。蛋白质靶向，因为其事件驱动的药理学不需要病毒的化学计量抑制蛋白质，因为有效蛋白质降解所需的亲和力通常较低。通过偶联特拉匹韦（FDA 批准的病毒抑制剂）开发了第一个小分子抗病毒降解剂丙型肝炎病毒 NS3-4A 蛋白酶与 CRBNCRL E3 泛素连接酶的配体生成的 NS3 降解剂。体外抑制 HCV，包括已知对 telaprevir 具有耐药性的点突变体。显示出对肠道病毒 2A 蛋白具有广谱活性，我们将在之前的工作基础上开发基于特拉匹韦的 2A 降解剂，从细胞中去除蛋白质并消除 2A 的所有功能。其次，我们将对与 2A 结合并抑制其作为介体功能的 DAA 进行高通量筛选这些筛选中发现的重要蛋白质-蛋白质相互作用的化合物将被验证为 2A 配体。并测试了抗病毒活性，并以经过验证的配体作为降解剂开发的先导物我们还将承担作为先导化合物开发的具有抗病毒活性的化合物。筛选 DNA 编码文库，以更广泛地采样化学空间并发现其他化学物质我们还将确定 DAA 是否靶向活性位点。（目标 1）和 2A 相互作用位点（目标 2）可以组合以获得卓越的功效和耐药性。这项工作利用了我们实验室在 TPD 和 2A 生物学领域的创新发现以及我们团队和 AViDD 在病毒学、药物化学、化学生物学生物化学、我们的工作是开发针对多功能 EV 2A 蛋白酶的 DAA。通过验证两种针对 2A 的新抗病毒机制并证明 TPD 作为抗病毒策略的效用。