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，是一种正义单链RNA病毒， 冠状病毒科SARS-CoV-2的RNA折叠成复杂的双螺旋结构， 为靶向RNA而非蛋白质的新型抗病毒方法打开了大门。正义RNA病毒 利用特殊折叠的RNA结构劫持宿主细胞的机器， 和mRNA翻译，逃避抗病毒反应，并产生更多的病毒颗粒。的机制 SARS-CoV-2和其他冠状病毒控制这些过程还不清楚。然而，在这方面， 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。这些基序作为病毒生命周期的功能开关， SARS-CoV-2致病机理的研究。在本申请中，我们提出使用三链体形成肽核酸， 酸（PNAs）来控制SARS-CoV-2假结的构象和生物学功能。很长的- 长期目标是（1）更好地了解SARS-CoV-2生物学和发病机制，（2）开发新的 以及针对多种冠状病毒株的广谱治疗剂。具体目标是：（1）研究 三链体形成的PNA对假结RNA开关的构象控制，以及（2）研究 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 目的是因为我们的研究小组一直致力于序列特异性识别的生物 重要的RNA分子使用三链体形成的PNA超过十年。拟议的研究是 这是一项重要的创新，因为人们对动态病毒RNA开关的生物学知之甚少， 在抗病毒治疗中尚未被广泛靶向。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，未来新的人类冠状病毒的出现是 几乎可以保证。突变的基因组可以被快速测序，使我们能够了解 突变改变了调控RNA基序的结构。靶向结构化的新型治疗剂 RNA基序将适用于对抗多种冠状病毒株，并且将易于调整， 突变的病毒，这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）突变PNA靶位点，所需的只是对突变的基因组进行测序 并改变治疗性三链体形成PNA的序列。RNA正在成为一种主要的调控因子， 分子在多种生物过程中发挥着重要作用，并成为一种有前途的新型治疗靶点。更好 了解病毒RNA开关的生物学作用， 创新的抗病毒方法来对抗SARS-CoV-2和其他冠状病毒。如果成功，则 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， 这将对我们防治当前和未来流行病的能力产生广泛和持续的影响。