Inhibiting Viral Macrodomains Using Structure-Based Design

使用基于结构的设计抑制病毒宏域

基本信息

批准号：
10512631
负责人：
James Solomon Fraser
金额：
$ 298.81万
依托单位：
UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
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/10512631
关键词：
2019-nCoV ADP ribosylation Address Adenosine Diphosphate Ribose Animal Model Animals Binding Biochemical Biochemistry Biological Assay Biological Markers COVID-19 treatment Catalogs Catalysis Cell Line Cell model Cells Chemicals Chemistry Chikungunya virus Communicable Diseases Computational Biology Computer Analysis Crystallography Defect Development Docking Drops Drug Design Drug Kinetics Drug Targeting Elements Feedback Foundations Future Head Human Immune response Immunofluorescence Immunologic Immunologics In Vitro Industrialization Infection Interferons Knowledge Lead Letters Measures Modeling Modification Monitor Mus Peptides Permeability Pharmaceutical Chemistry Pharmaceutical Preparations Post-Translational Protein Processing Property Proteins Proteomics Reporting Roentgen Rays SARS coronavirus Side Signal Pathway Signal Transduction Specificity Structure Testing Toxicology Transgenes Viral Viral Load result Virus Virus Diseases Work X-Ray Crystallography analog base cellular targeting computational chemistry design effectiveness testing experimental study human disease in vivo inhibitor mutant pandemic disease phosphoproteomics programs response scaffold screening side effect structural biology targeted biomarker therapeutic evaluation tool transcriptome sequencing virology

项目摘要

PROJECT 5: INHIBITING VIRAL MACRODOMAINS USING STRUCTURE-BASED DESIGN SUMMARY Viral macrodomains counter the host immune response by removing ADP-ribosylation modifications from host proteins, with important consequences for interferon and many other signaling pathways. Previous experiments in cell and animal models that use wild type and catalytically dead SARS-CoV and chikungunya virus (CHIKV) macrodomains validate these proteins as potential drug targets. However, no inhibitors exist for viral macrodomains. Using an integration of high throughput X-ray based fragment screen and docking, we have identified over 200 binders to the SARS-CoV-2 macrodomain (Mac1). Our subsequent assays guided the development of the first structurally characterized tool compounds that are more potent than the substrate ADP- ribose. In addition, we have leveraged the chemical knowledge to uncover additional scaffolds by docking. In this proposal, we advance compounds through a structure-based design approach, using biochemical assays against peptide binding and catalytic function. To identify starting points against the CHIKV macrodomain, we will perform a new X-ray crystallography-based fragment screen and perform an Ultra-large docking campaign (Screening Core). Our plan is to design compounds with low potency against human macrodomains and to leverage medicinal chemistry to drive potency against viral macrodomains. Our early activities will identify multiple alternative scaffolds with high potency in vitro to progress to target engagement in cells. Our cell-based aims will use cellular thermal shift and immunofluorescence of interferon treated cells as early markers of target engagement (Proteomics Core, In Vitro Virology Core). We will identify biomarkers by comparing RNAseq, proteomics, phosphoproteomics and ADP-Ribosylation AP-MS of compound treated cells to mutant macrodomains (both as a transgene and in the context of virus). During these activities, we will continue addressing aspects of permeability, off target effects, and other liabilities with the Medicinal Chemistry Core. We will progress to animal models compounds with cellular effects on replication with validated target engagement. Lead molecules with validated target engagement and minimal pharmacokinetic liabilities will allow us to test the effectiveness of candidate molecules in animal models of SARS-CoV-2 and CHIKV (In Vivo Virology Core). Based on previous studies in animal models with catalytically inactive macrodomain mutant viruses, we will prioritize molecules that drop viral load by at least 100-fold. Our work will generate a target package for further development by our industrial partner, Roche. The lessons of targeting SARS-CoV-2 and CHIKV macrodomains will be applicable to developing future agents against macrodomains in other viruses and those implicated in human disease.

项目5：使用基于结构的设计抑制病毒大域概括病毒宏domain通过去除宿主的ADP-核糖基化修饰来对抗宿主免疫反应蛋白质，对干扰素和许多其他信号通路产生重要影响。先前的实验在使用野生型和催化死亡的SARS-COV和Chikungunya病毒（CHIKV）的细胞和动物模型中大域验证这些蛋白质是潜在的药物靶标。但是，不存在病毒抑制剂大域。使用高吞吐量基于X射线的片段屏幕和对接的集成，我们有鉴定出200多个与SARS-COV-2宏域（MAC1）的粘合剂。我们随后的测定指导开发第一个结构表征的工具化合物，该化合物比底物ADP- 核糖。此外，我们还利用化学知识来通过对接来发现其他脚手架。在该建议，我们使用生化测定法通过基于结构的设计方法提高化合物针对肽结合和催化功能。为了识别针对Chikv Macrodomain的起点，我们将执行新的基于X射线晶体学的片段屏幕并执行超大对接活动（筛选核心）。我们的计划是设计对人类大域的效力低下的化合物和利用药物化学来推动对病毒宏构域的效力。我们的早期活动将确定体外具有高效力的多个替代脚手架以进展到靶向细胞。我们的基于单元的 AIMS将使用干扰素处理细胞的细胞热偏移和免疫荧光作为目标的早期标记参与（蛋白质组学核心，体外病毒学核心）。我们将通过比较RNASEQ来识别生物标志物，化合物处理细胞的蛋白质组学，磷蛋白质组学和ADP-核糖基化AP-MS 宏域（无论是转基因还是病毒的背景）。在这些活动中，我们将继续通过药物化学核心解决渗透率，关闭目标效应和其他负债的各个方面。我们将发展为具有细胞对复制作用的动物模型化合物，并具有经过验证的目标订婚。具有验证目标参与和最少药代动力学负债的铅分子将允许我们测试候选分子在SARS-COV-2和CHIKV动物模型中的有效性（体内病毒学核心）。基于先前在具有催化性障碍大域突变体的动物模型中的研究病毒，我们将优先考虑将病毒负荷下降至少100倍的分子。我们的工作将产生目标我们的工业合作伙伴罗氏（Roche）的进一步发展方案。定位SARS-COV-2和 CHIKV宏域将适用于在其他病毒和那些与人类疾病有关的人。