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

• 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
• 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

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：小分子抑制剂和picornavirus 2a蛋白酶的降解器 传统的直接作用抗病毒药（DAAS）通过占据酶袋来靶向病毒蛋白；解离 药物的中断导致立即保留功能。因此，大多数抗病毒药必须具有高亲和力， 化学计量结合至有效，而减少亲和力的点突变会迅速引起抗病毒 反抗。预防抗性的既定方法是使用直接作用抗病毒药的组合 该行动通过独立的目标和机制。在这个项目中，我们将采取两种创新的方法 开发靶向肠病毒（EV）2a蛋白酶的DAA，这是一种至少两个基本功能的病毒蛋白：（1） 它催化病毒多蛋白的必需切割，（2）介导蛋白质 - 蛋白质相互作用 复制至关重要。首先，我们将追求针对2a作为抗病毒的靶向蛋白质降解（TPD） 战略。 TPD是药物开发的新范式，其中一个小分子结合了感兴趣的目标 与E3连接酶配体共轭，导致蛋白质降解。这种方法允许更广泛的范围 蛋白质靶标，因为其事件驱动的药理学不需要对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。我们以前 通过耦合telaprevir（一种经FDA批准的抑制剂）开发了第一个小分子抗病毒降解器 丙型肝炎病毒NS3-4A蛋白酶，到CRBNCRL E3泛素连接酶的配体。由此产生的NS3降解器 在体外抑制HCV，包括已知可以抗尾能抗性的点突变体。由于最近是Telaprevir 证明对肠病毒2A蛋白具有广泛的活动，我们将以先前的工作为基础 开发基于2a的telaprevir降解器，从而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进行高通量屏幕 基本蛋白质 - 蛋白质相互作用。这些屏幕中发现的化合物将被验证为2a配体 并测试了抗病毒活性的测试，已有验证的配体高级作为降解器发育和 具有抗病毒活性的化合物作为DAA开发的铅化合物。我们还将承担 筛选DNA编码的库以更广泛的化学空间采样，并发现其他化学物质 适用于抑制剂和降解器开发的物质。我们还将确定DAA是否针对活动位点 （AIM 1）和2A相互作用位点（AIM 2）可以合并，以提高效率和电阻曲线。这 工作利用了我们的实验室在TPD和2A生物学领域的创新发现以及 我们群体的集体专业知识和病毒学，药物化学，化学生物学生物化学的avidd， 结构生物学和药物发现。我们开发针对多功能EV 2A蛋白酶的DAA的工作 通过验证两个新的抗病毒机制来靶向2a并通过证明，将产生广泛的影响 TPD作为抗病毒策略的实用性。