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: 10618786
• 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/10618786
• 关键词: Address; Affect; Antiviral Agents; Binding; Biological Assay; Capsid; Capsid Proteins; Cells; Cessation of life; Chronic Hepatitis B; Cirrhosis; 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; Learning; Liver; Malignant Neoplasms; Methods; Modification; Molecular Conformation; Morbidity - disease rate; Outcome; Pathway interactions; Persons; Procedures; Process; Property; Protein Conformation; Protein Dynamics; Protein Inhibition; Proteins; Rationalization; Resistance; Reverse Transcription; Sampling; Structure; Synthesis Chemistry; Testing; Toxic effect; United States; Viral; Viral Genome; Viral Physiology; Virus; Virus Assembly; Virus Diseases; clinically relevant; dimer; drug development; experimental study; improved; intermolecular interaction; lead optimization; machine learning classification; molecular dynamics; mortality; novel; novel therapeutics; pathogen; pathogenic virus; pharmacologic; 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.

项目总结/摘要 病毒是世界范围内发病率和死亡率的主要原因之一，其中B型肝炎病毒（HBV）是 其中最具传染性和流行性的一种。全世界约有2.5亿人患有慢性 HBV感染，其中1-2万在美国。在感染者中，大约15-25%的人会发展为SE- 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。而 目前存在治疗慢性HBV感染的疗法，所有疗法都靶向病毒基因组过程，如逆转录， 和DNA复制，但由于病毒的持久性和耐药性，没有一种能治愈。一个有前途的正交 消除感染的方法是靶向HBV的衣壳，即包裹病毒基因组的蛋白质外壳。 Finn实验室先前已经开发出了诱导非功能性聚合物错误组装的化合物。 HBV衣壳，表明小分子有能力影响这些大的多蛋白质的结构 组件.虽然对这些化合物的分子间相互作用的结构了解很多， 事实上，艾德在事后被发现，很少有人探索这种相互作用的动力学，而且预测性不足， 功能性（抗病毒）结合的标准还有待开发。这两个缺陷将开始得到解决， 这个戒酒会这使用分子动力学（MD）模拟结合HepAD 38细胞的体外实验， PI已经鉴定了艾德七种基于先前未知的与HBV相互作用的基序的化合物， 衣壳组装过程。这些化合物结合在两个衣壳蛋白（Cp）界面处的已知口袋中， 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，自由能微扰， 化学和合成化学，PI将优化先导化合物，以提高其对HBV的有效性。在 第二个目标是利用分子动力学模拟、先进的自由能计算和实验分析 在不同的HBV蛋白寡聚体上，直到并包括整个病毒衣壳，PI将确定 分子干扰衣壳装配。这两个目标都将贝内于使用基于机器学习的分类， 阳离子方案以及新的增强采样方法。这里学到的教训是， 分子可以将组装途径重定向为非生产性构象， 其他病毒。