Targeting SARS-CoV-2 RNA Pseudoknots Using Triplex-Forming Peptide Nucleic Acids

使用三链体​​形成肽核酸靶向 SARS-CoV-2 RNA 假结

• 批准号: 10328839
• 负责人: ERIKS ROZNERS
• 金额: $ 19.45万
• 依托单位: STATE UNIVERSITY OF NY,BINGHAMTON
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-11-01 至 2023-10-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10328839
• 关键词: 2019-nCoV; 3' Untranslated Regions; 5' Untranslated Regions; Affect; Aminopyridines; Antiviral Agents; Antiviral Response; Antiviral Therapy; Back; Binding; Biological; Biological Process; Biology; COVID-19; Calorimetry; Cartoons; Cations; Cells; Chemicals; Complex; Coronavirus; Cultured Cells; Detection; Double-Stranded RNA; Family; Future; Genetic Transcription; Genetic Translation; Genome; Goals; Health Technology; Human; Hydrogen Bonding; Lead; Life Cycle Stages; Messenger RNA; Molecular Conformation; Mutate; Mutation; Nucleic Acid Binding; Pathogenesis; Peptide Nucleic Acids; Physiological; Positioning Attribute; Process; Protein Biosynthesis; Proteins; RNA; RNA Conformation; RNA Folding; RNA Stability; RNA Viruses; RNA chemical synthesis; Replicon; Reporter; Research; Role; SARS-CoV-2 pathogenesis; Site; Structure; Testing; Therapeutic; Thermodynamics; Translations; Viral; Viral Genome; Viral Packaging; Viral Physiology; Viral Proteins; Virus; Virus Replication; base; combat; fighting; gel mobility shift assay; human coronavirus; innovation; new therapeutic target; novel; novel therapeutics; nucleobase; pandemic disease; particle; pathogen; peptide structure; protein expression; response; targeted treatment; tool; triple helix; viral RNA

SARS-CoV-2, the causative agent of COVID-19, is a positive-sense single-stranded RNA virus in the Coronaviridae family. The RNA of SARS-CoV-2 folds into complex double-helical structures that open the door for novel anti-viral approaches targeting RNA instead of proteins. Positive-sense RNA viruses use the specifically folded RNA structures to highjack the host cell's machinery, regulate viral replication and mRNA translation, evade antiviral responses, and produce more viral particles. The mechanisms by which SARS-CoV-2 and other coronaviruses control these processes are not well understood. However, highly conserved structural motifs of viral RNA, such as pseudoknots and hairpins, are critical for replication and translation. These motifs act as functional switches of the viral life cycle and are critical for SARS-CoV-2 pathogenesis. In this application, we propose to use triplex-forming peptide nucleic acids (PNAs) to control the conformation and biological function of SARS-CoV-2 pseudoknots. The long- term goals are to (1) better understand SARS-CoV-2 biology and pathogenesis and (2) develop new and broad-spectrum therapeutics against multiple coronavirus strains. The specific aims are to (1) study the conformational control of pseudoknot RNA switches with triplex-forming PNA and (2) study how the PNA binding and RNA switching affects coronavirus biology. We are well positioned to achieve these Aims because our research group has been working on sequence-specific recognition of biologically significant RNA molecules using triplex-forming PNAs for more than a decade. The proposed research is significant and innovative because the biology of dynamic viral RNA switches is poorly understood and have not been widely targeted in antiviral therapy. Coronaviruses can mutate their RNA genome and cross species boundaries to infect humans. Therefore, future emergence of new human coronaviruses is almost guaranteed. Mutated genomes can be rapidly sequenced, allowing us to understand how the mutations change the structure of regulatory RNA motifs. Novel therapeutic agents targeting structured RNA motifs will be applicable against multiple strains of coronaviruses and will be easily adjustable for mutated viruses, which is a key bottleneck for traditional antiviral therapeutics. If SARS-CoV-2 (or another coronavirus) mutates the PNA target site, all that is needed is to sequence the mutated genome and change the sequence of therapeutic triplex-forming PNA. RNA is emerging as a major regulatory molecule in wide variety of biological processes and as a promising novel therapeutic target. Better understanding of the biological role of viral RNA switches holds tremendous promise to result in innovative antiviral approaches to combat SARS-CoV-2 and other coronaviruses. If successful, the proposed research will develop new tools for studying the biology of complex regulatory viral RNAs, which will have broad and sustained impact on our ability to combat the current and future pandemics.

SARS-CoV-2 是 COVID-19 的病原体，是一种正链单链 RNA 病毒。 冠状病毒科。 SARS-CoV-2 的 RNA 折叠成复杂的双螺旋结构，打开 为针对 RNA 而不是蛋白质的新型抗病毒方法打开了大门。正义RNA病毒 使用特定折叠的RNA结构劫持宿主细胞的机器，调节病毒复制 和 mRNA 翻译，逃避抗病毒反应，并产生更多的病毒颗粒。其机制由 SARS-CoV-2 和其他冠状病毒控制这些过程的机制尚不清楚。然而， 病毒 RNA 的高度保守的结构基序，如假结和发夹，对于 复制和翻译。这些基序充当病毒生命周期的功能开关，并且至关重要 SARS-CoV-2 发病机制。在此应用中，我们建议使用三链体​​形成肽核酸 酸（PNA）来控制 SARS-CoV-2 假结的构象和生物学功能。长- 术语目标是 (1) 更好地了解 SARS-CoV-2 生物学和发病机制，以及 (2) 开发新的 以及针对多种冠状病毒株的广谱疗法。具体目标是 (1) 研究 假结 RNA 开关与三链体形成 PNA 的构象控制，以及 (2) 研究如何 PNA 结合和 RNA 转换影响冠状病毒生物学。我们有能力实现这些目标 目标是因为我们的研究小组一直致力于生物学上的序列特异性识别 十多年来，人们一直在使用形成三链体的 PNA 来研究重要的 RNA 分子。拟议的研究是 意义重大且具有创新性，因为人们对动态病毒 RNA 开关的生物学知之甚少， 尚未广泛用于抗病毒治疗。冠状病毒可以使其 RNA 基因组发生突变， 跨越物种界限感染人类。因此，未来新型人类冠状病毒的出现是 几乎可以保证。突变的基因组可以快速测序，使我们能够了解突变基因组是如何发生的。 突变改变了调控RNA基序的结构。靶向结构的新型治疗剂 RNA 基序将适用于对抗多种冠状病毒株，并且可以轻松调整 变异病毒是传统抗病毒疗法的关键瓶颈。如果 SARS-CoV-2（或 另一种冠状病毒）使 PNA 目标位点发生突变，所需要做的就是对突变的基因组进行测序 并改变治疗性三联体形成 PNA 的序列。 RNA正在成为一种主要的调控手段 分子在多种生物过程中的作用，并作为有前途的新型治疗靶点。更好的 了解病毒 RNA 开关的生物学作用有望带来巨大的希望 对抗 SARS-CoV-2 和其他冠状病毒的创新抗病毒方法。如果成功的话， 拟议的研究将开发新的工具来研究复杂的调节病毒 RNA 的生物学， 这将对我们抗击当前和未来流行病的能力产生广泛和持续的影响。