Altering Hepatitis B Virus assembly through pharmacological intervention

通过药物干预改变乙型肝炎病毒组装

• 批准号: 10394388
• 负责人: James C. Gumbart
• 金额: $ 39.31万
• 依托单位: GEORGIA INSTITUTE OF TECHNOLOGY
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-05-06 至 2025-04-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10394388
• 关键词: Address; Affect; Antiviral Agents; Binding; Biological Assay; Capsid; Capsid Proteins; Cations; Cells; Cessation of life; Chronic Hepatitis B; Cirrhosis; Classification; Classification Scheme; Complex; Computer Simulation; Coupled; Cryoelectron Microscopy; DNA biosynthesis; Development; Docking; Encapsulated; Equilibrium; Failure; Free Energy; Goals; HIV-1; Health; Hepatitis B Virus; Human; Image; In Vitro; Infection; Intervention; Knowledge; Laboratories; Lead; Liver; Machine Learning; Malignant Neoplasms; Methods; Modification; Molecular Conformation; Morbidity - disease rate; Outcome; Pathway interactions; Persons; Pharmacology; Procedures; Process; Property; Protein Conformation; Protein Dynamics; Resistance; Reverse Transcription; Sampling; Scheme; Structure; Synthesis Chemistry; Testing; Toxic effect; United States; Viral; Viral Genome; Virus; Virus Assembly; Virus Diseases; base; clinically relevant; dimer; drug development; experimental study; improved; intermolecular interaction; lead optimization; machine learning classification; molecular dynamics; mortality; novel; novel therapeutics; pathogenic virus; programs; protein oligomer; protein protein interaction; protein structure; rational design; simulation; small molecule; success; viral genomics

Project Summary/Abstract Viruses are one of the leading causes of morbidity and mortality worldwide, with Hepatitis B Virus (HBV) being one of the most infectious and prevalent among them. Roughly 250 million people worldwide suffer from chronic HBV infection, including 1-2 million in the United States. Of those infected, approximately 15-25% will develop se- rious liver problems, including cirrhosis, cancer, and ultimately failure, leading to 600,000 deaths annually. While therapies exist to manage chronic HBV infection, all target viral genomic processes such as reverse transcription and DNA replication, and none provide a cure due to viral persistence and resistance. A promising orthogonal approach to eliminating infection is to target HBV's capsid, the protein shell that encapsulates the viral genome. The Finn laboratory has previously developed compounds that induce the misdirected assembly of non-functional HBV capsids, showing that small molecules have the power to affect the structures of these large multi-protein assemblies. While much is known about the structures of the intermolecular interactions with these compounds identified after the fact, little about the dynamics of such interactions has been explored, and a predictive under- standing of functional (antiviral) binding has yet to be developed. Both deficiencies will begin to be addressed in this program. Using molecular dynamics (MD) simulations coupled with in vitro experiments on HepAD38 cells, the PIs have identified seven compounds based on motifs previously unknown to interact with HBV that target the capsid assembly process. These compounds bind in a known pocket at the interface of two capsid-protein (Cp) dimers, possess moderate antiviral activity, and low toxicity. In the first aim, using docking, free-energy perturba- tion, and synthetic chemistry, the PIs will optimize the lead compound to improve its efficacy against HBV. In the second aim, using molecular dynamics simulations, advanced free-energy calculations, and experimental assays on different HBV protein oligomers, up to and including the whole virus capsid, the PIs will determine how small molecules interfere with capsid assembly. Both aims will benefit from using a machine-learning-based classifi- cation scheme as well as novel enhanced sampling methods. The lessons learned here concerning how small molecules can re-direct the assembly pathway into unproductive conformations can be generalized for application to other viruses.

项目概要/摘要 病毒是全世界发病和死亡的主要原因之一，其中乙型肝炎病毒 (HBV) 其中最具传染性和最流行的疾病之一，全世界约有 2.5 亿人患有慢性病。 乙型肝炎病毒感染者（包括美国的 1-200 万人）中，大约有 15-25% 会出现感染。 严重的肝脏问题，包括肝硬化、癌症和最终的衰竭，每年导致 60 万人死亡。 存在治疗慢性乙型肝炎感染的疗法，所有疗法都针对病毒基因组过程，例如逆转录 和 DNA 复制，但由于病毒的持久性和耐药性，没有一种方法能提供治愈方法。 消除感染的方法是针对乙型肝炎病毒的衣壳，即封装病毒基因组的蛋白质外壳。 芬恩实验室此前已开发出能够诱导非功能性分子错误组装的化合物。 HBV 衣壳，表明小分子有能力影响这些大型多蛋白的结构 虽然人们对这些化合物的分子间相互作用的结构了解很多。 事后发现，人们对这种相互作用的动态知之甚少，并且预测不足 功能性（抗病毒）结合的地位尚未得到发展，这两个缺陷将在 2017 年开始得到解决。 该程序使用分子动力学 (MD) 模拟结合 HepAD38 细胞的体外实验， PI 已根据先前未知的与 HBV 相互作用的基序，鉴定出七种化合物，这些化合物针对 这些化合物结合在两个衣壳蛋白 (Cp) 界面的已知口袋中。 二聚体，具有中等的抗病毒活性和低毒性。在第一个目标中，使用对接、自由能扰动。 化和合成化学方面，PI 将优化先导化合物，以提高其对抗 HBV 的效率。 第二个目标，使用分子动力学模拟、先进的自由能计算和实验分析 对于不同的 HBV 蛋白寡聚体，直至并包括整个病毒衣壳，PI 将决定多小 分子干扰衣壳组装。这两个目标都将受益于使用基于机器学习的分类。 阳离子方案以及新颖的增强抽样方法在这里吸取的教训是关于多小的。 分子可以将组装途径重新引导为非生产性构象，可以推广应用 到其他病毒。