Programming designer DNA nanostructures for blocking enveloped viral infection

编程设计 DNA 纳米结构以阻止包膜病毒感染

基本信息

批准号：
10598739
负责人：
Weishan Huang
金额：
$ 20.31万
依托单位：
LOUISIANA STATE UNIV A&M COL BATON ROUGE
依托单位国家：
美国
项目类别：
财政年份：
2023
资助国家：
美国
起止时间：
2023-07-14 至 2025-06-30
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10598739
关键词：
2019-nCoV ACE2 Agar Gel Electrophoresis Animal Model Antigens Antiviral Therapy Area Atomic Force Microscopy Avidity Binding Biological Assay COVID-19 Cell model Cells Characteristics Collection DNA Detection Development Dose Effectiveness Engineering Epithelial Cells Epitopes Etiology Exhibits Goals HIV Human In Vitro Infection Influenza Knock-in Mouse Knowledge Lung Mechanics Medicine Membrane Glycoproteins Membrane Proteins Molecular Molecular Genetics Nanostructures Nanotechnology Pattern Positioning Attribute Preventive Price Property Proteins Resistance Route SARS-CoV-2 B.1.1.529 SARS-CoV-2 B.1.617.2 SARS-CoV-2 P.1 SARS-CoV-2 infection SARS-CoV-2 inhibitor SARS-CoV-2 spike protein SARS-CoV-2 variant Safety Sensitivity and Specificity Series Shapes Structure Surface Technology Testing Therapeutic Toxic effect United States National Institutes of Health Validation Viral Virion Virus Virus Diseases Work anti-viral efficacy antiviral drug development aptamer biomaterial compatibility cost cost estimate cytotoxic cytotoxicity design drug development flexibility future epidemic genetic technology in vivo innovation innovative technologies mimicry mouse model nano nanobodies nanoscale pandemic disease particle pathogen post SARS-CoV-2 infection precision medicine prevent programs prophylactic prototype receptor receptor binding screening transmission process variants of concern viral entry inhibitor

项目摘要

Project Summary/Abstract SARS-CoV-2, the etiological pathogen of COVID-19, has resulted in a pandemic. There remains an urgent need for innovative technologies which facilitate the development of affordable antiviral precision medicine. SARS-CoV-2 is an enveloped virus, and the structure of the trimeric spike protein clusters on the virion has been solved. To develop innovative, affordable, and biocompatible antiviral candidates against SARS-CoV-2 infection and transmission, we exploited the structural characteristics of viral surface proteins that can be matched at nanoscale precision by engineered DNA nanostructure platforms. Based on the structure of the SARS-CoV-2 virion and surface spike trimer layout, we have synthesized a designer DNA nanostructure (DDN) that takes the form of a macromolecular ‘net’ whose vertices are a precise mechanical match to the spacing and positioning of the spike protein matrix displayed on the virus outer surface. We hypothesize that the structural properties and the layout patterns of SARS-CoV-2 spike proteins can be exploited to design DDNs with nanoscale precision which are capable of matching and capturing intact SARS-CoV-2 virions with ultrahigh binding avidity and selectivity, thereby blocking SARS-CoV-2 infection. We have screened and found DNA aptamers and nanobodies that are specific for the spike receptor-binding domain (RBD). These spike binders can be incorporated into the ‘knots’ of the DDN net to allow the simultaneous binding of multiple DNA aptamers with multiple spikes on the viral surface in a polyvalent, pattern-matching fashion. The DNA ‘net’-aptamer prototype construct has afforded dramatic increase in SARS-CoV-2 binding avidity. This construct can work as a decoy to block viral entry into host cells and is about 1,000-fold more potent than the free aptamer. In this R21 proposal, we aim to extend this technology to enable the incorporation of multiple types of probes against spike RBD and to validate the safety and effectiveness of DDNs in antiviral therapy in vitro and in vivo. We propose two specific aims: to (1) design, synthesize, validate, and further optimize the virus-capturing avidity against various SARS- CoV-2 variants of concern (VOCs); and (2) to determine the antiviral potency and cytotoxicity of the designed DDNs during SARS-CoV-2 infections in vitro in human lung epithelial cells and in vivo in human ACE2-knockin mice. Completion of this work will help us define the antiviral potency and safety of the DNA nanostructures that are designed to perfectly match epitope layouts on the viral surface to capture and wrap live viruses. The estimated cost of DDN treatment is approximately $10/dose (a price that likely decreases at large-scale synthesis), making it an affordable therapy. This DDN platform may further contribute to the rapid development of antiviral precision medicine against emerging SARS-CoV-2 VOCs, as well as other enveloped viruses such as influenza and HIV.

项目概要/摘要 SARS-CoV-2（COVID-19 的病原体）已导致大流行，目前仍处于紧急状态。需要创新技术来促进开发负担得起的抗病毒精准医学。 SARS-CoV-2是一种有包膜病毒，病毒粒子上的三聚体刺突蛋白簇的结构已被研究开发针对 SARS-CoV-2 感染的创新、经济实惠且生物相容的抗病毒候选药物。和传播，我们利用了病毒表面蛋白的结构特征，可以在基于 SARS-CoV-2 结构的工程 DNA 纳米结构平台实现纳米级精度。病毒粒子和表面刺突三聚体布局，我们合成了一种设计DNA纳米结构（DDN），它采用高分子“网”的形式，其顶点与分子的间距和定位精确机械匹配显示在病毒外表面上的刺突蛋白基质。 SARS-CoV-2刺突蛋白的布局模式可用于设计纳米级精度的DDN 能够以超高的结合亲合力匹配和捕获完整的 SARS-CoV-2 病毒粒子，选择性，从而阻断SARS-CoV-2感染，我们筛选并发现了DNA适体并这些尖峰结合物可以是对尖峰受体结合结构域(RBD)具有特异性的纳米抗体。整合到 DDN 网络的“结”中，以允许多个 DNA 适体同时结合以多价、模式匹配的方式在病毒表面形成多个尖峰。该构建体显着增加了 SARS-CoV-2 的结合亲和力。该构建体可以作为诱饵。阻止病毒进入宿主细胞，其效力比游离适体强约 1,000 倍。我们的目标是扩展这项技术，以便能够结合多种类型的探针来对抗尖峰 RBD 和为了验证 DDN 在体外和体内抗病毒治疗中的安全性和有效性，我们提出了两种具体方案。目标：（1）设计、合成、验证并进一步优化针对各种 SARS 的病毒捕获亲和力关注的 CoV-2 变体 (VOC)；以及 (2) 确定设计的抗病毒效力和细胞毒性人肺上皮细胞体外 SARS-CoV-2 感染期间的 DDN 以及人 ACE2 敲入体内的 DDN 完成这项工作将有助于我们确定 DNA 纳米结构的抗病毒效力和安全性。旨在完美匹配病毒表面的表位布局，以捕获和包裹活病毒。 DDN 治疗的估计费用约为 10 美元/剂（该价格可能会大规模下降）合成），使其成为一种负担得起的疗法，该 DDN 平台可能会进一步促进快速发展。针对新出现的 SARS-CoV-2 VOC 以及其他包膜病毒的抗病毒精准医学如流感和艾滋病毒。