Inducing Off-pathway Assembly of HIV Gag Polyprotein with Computationally Designed Peptides

病毒是在宿主细胞内构建的无生命生物分子组合，用于 传播和感染。尽管产生功能性传染病所需的高度保真度 颗粒，病毒擅长对自然和疫苗诱导的免疫反应产生抵抗力 通过逃逸突变。这是由于存在多个冗余自组装信号， 从而形成具有大片有利序列空间的适合度景观。病毒可以提取样本 从这个空间广泛地到达转义变种，同时保留适当的能力 集合。 我们提出了一种变革性的方法，旨在针对大范围的病毒适应 景观，目标是克服抗病毒药物耐药性。在这种方法中，各种病毒 自组装信号将被用来诱导病毒组件的错误组装，使之成为非 感染性终结点。经过计算设计的多肽将引导自组装过程走向 大量遗传变异所能达到的囚禁状态。多肽是这项任务的理想选择，对于 原因有很多。首先，多肽可以靶向蛋白质的大表面积，允许结合到 缺乏雄厚财力的目标。其次，多肽可以被设计成自组装成 不同的超分子结构，如纤维、二维阵列和液体冷凝物。我们 将利用多肽形成这些类型的结构的能力来诱导非 传染性病毒错误组装。最后，可以优化多肽的膜通透性，从而 用于靶向宿主细胞内的病毒复制。 药物诱导的HIV病毒衣壳错误组装被认为是几种可能的可能性之一 小分子药物PF74的作用机制。我们的目标是开发一种合理指导的设计 使这一新的抗病毒作用机制得以广泛应用的途径。我们会 靶向HIV Gag蛋白的三个已知结构域，它们在病毒组装中发挥不同的作用 通过计算设计的多肽进行错误组装。 由此产生的多肽将包含指导捕获病毒成分的设计元素 在一维纤维、二维阵列和三维液体冷凝物中。自我- 将使用干涉质谱仪在单分子水平上监测组装情况，以及 在体层水平上用生物层干涉和动态光散射，而在电子显微镜下 并将使用荧光显微镜来可视化诱导的组装。该项目为 通过对抗病毒构成高障碍的机制开发抗病毒疗法的途径 抵抗。

Viruses are inanimate biomolecular assemblages constructed inside host cells for the tasks of transmission and infection. Despite the high degree of fidelity required to produce functional infectious particles, viruses are adept at developing resistance to natural and vaccine-induced immune responses through escape mutations. This is due to the presence of multiple redundant self-assembly signals, resulting in a fitness landscape with vast regions of favorable sequence space. Viruses can sample extensively from this space to arrive at escape variants, while retaining the capacity to properly assemble. We propose a transformative approach that aims to target large regions of viral fitness landscapes, with the goal of overcoming antiviral drug resistance. In this approach, various viral self-assembly signals will be exploited to induce the mis-assembly of viral components toward non- infectious endpoints. Computationally designed peptides will steer the self-assembly process toward trapped states accessible to large numbers of genetic variants. Peptides are ideal for this task for a number of reasons. Firstly, peptides can target large surface areas of proteins, allowing for binding to targets that lack deep binding pockets. Secondly, peptides can be designed to self-assemble into diverse supramolecular structures, such as fibers, two-dimensional arrays, and liquid condensates. We will leverage the ability of peptides to form these types of structures to induce the formation of non- infectious viral mis-assemblies. Finally, peptides can be optimized for membrane permeability, allowing for the targeting of viral replication inside host cells. Drug-induced mis-assembly of HIV viral capsid has been suggested as one of several possible mechanisms of action of the small-molecule drug PF74. We aim to develop a rationally-guided design approach to enable the wide-spread application of this novel mechanism of anti-viral action. We will target three domains of the HIV Gag protein known to play distinct roles in viral assembly for directed mis-assembly by computationally designed peptides. The resulting peptides will incorporate design elements that direct the trapping of viral components within one-dimensional fibers, two-dimensional arrays, and three-dimensional liquid condensates. Self- assembly will be monitored at the single-molecule level using Interferometric Mass Spectrometry, and at the bulk level with Bio-layer Interferometry and Dynamic Light Scattering, while Electron Microscopy and Fluorescence Microscopy will be used to visualize the induced assemblies. This project paves the way for development of antiviral therapies through mechanisms that pose high barriers to antiviral resistance.