Developing three-dimensional antisense oligonucleotide drugs against COVID-19

项目摘要(摘要) 抗新冠肺炎三维反义寡核苷酸药物的研制 冠状病毒病2019年(新冠肺炎)大流行的元凶，与严重急性呼吸系统综合症有关 冠状病毒-2(SARS-CoV-2)具有一个非常大的RNA基因组，编码蛋白质和RNA元件 病毒感染和复制的方方面面都需要。这一属性使病毒容易受到新类别的攻击 称为反义寡核苷酸(ASO)的药物。ASO是一种单链合成核酸，可以实现 通过Watson-Crick碱基配对与病毒或其他靶RNA结合的治疗效果，正是这种相互作用 这定义了分子生物学和生命的基础。美国食品和药物管理局批准的第一种ASO药物 给药是一种抗巨细胞病毒的药物。开发ASO抗病毒药物的一个主要挑战是 RNA折叠成干扰ASO杂交的结构的强烈趋势。当前ASO设计 方法不能充分解决这个问题。 我们开发了一个基于结构的ASO设计技术平台，该平台利用了三个方面的优势： 靶RNA的空间结构。我们的3D-ASO不仅能识别序列，还能识别形状 SARS-CoV-2 RNA。与传统设计相比，3D-ASO与病毒RNA的接触更广泛， 因此可以达到更大的亲和力和特异性。我们的技术平台包括四个设计模板和 采用创新的RNA结构确定方法的3D-ASO药物开发工作流程。在一个 初步研究，我们设计并测试了几种抗SARS-CoV-2病毒RNA的3D-ASO，并鉴定了两种 在培养的人类细胞中强烈抑制病毒复制的前导序列比 先前报道的序列。在拟议的研究中，我们将通过改变其主导性3D-ASO的 骨架修饰和碱基，可更紧密地结合，更适合病毒RNA，并具有更强的抑制作用 他们的职能。我们还将通过设计和测试更多的抗SARS-CoV-2 3D-ASO来撒下我们的网。 最后，最有效的3D-ASO将在动物模型中进行测试。如果成功，该项目将提供ASO 临床试验的候选药物。这些药物可以鼻腔喷雾或静脉注射的形式给药，如 治疗或预防。我们将提炼的基于结构的设计技术普遍适用于ASO 药物开发。因此，这项研究有潜力扭转对抗新冠肺炎和 在我们与许多其他疾病的斗争中。

Project Summary (Abstract) Developing three-dimensional antisense oligonucleotide drugs against COVID-19 The culprit of coronavirus disease 2019 (COVID-19) pandemic, severe acute respiratory syndrome-related coronavirus-2 (SARS-CoV-2), has a very large RNA genome that encodes the proteins and RNA elements required for all aspects of viral infection and replication. This property makes the virus vulnerable to a new class of drugs called antisense oligonucleotide (ASO). ASOs are single-stranded synthetic nucleic acids that achieve therapeutic effects by binding to viral or other target RNAs via Watson-Crick base pairing, the very interaction that defines molecular biology and the foundation of life. The first ASO drug approved by the U.S. Food and Drug Administration is an antiviral against cytomegalovirus. A major challenge of developing ASO antiviral drugs is the strong tendency of RNA to fold into structures that interfere with ASO hybridization. Current ASO design methods do not adequately address this problem. We have developed a structure-based ASO design technology platform that takes advantage of three- dimensional structures of target RNAs. Our “3D-ASOs” recognize not only the sequences but also the shapes of SARS-CoV-2 RNAs. Compared to conventional designs, 3D-ASOs contact viral RNAs more extensively and therefore can achieve greater affinity and specificity. Our technology platform includes four design templates and a 3D-ASO drug development workflow that employs an innovative RNA structure determination method. In a preliminary study, we designed and tested several 3D-ASOs against SARS-CoV-2 viral RNA and identified two lead sequences that strongly inhibit viral replication in cultured human cells to a much greater extent than previously reported sequences. In the proposed research, we will optimize the lead 3D-ASOs by altering their backbone modifications and bases for tighter binding and better fit to the viral RNAs and for stronger inhibition to their functions. We will also cast our net wide by designing and testing additional anti-SARS-CoV-2 3D-ASOs. Finally, the most potent 3D-ASOs will be tested in an animal model. If successful, the project will provide ASO drug candidates for clinical trials. These drugs may be given as nasal sprays or via intravenous injection, as treatments or for prevention. The structure-based design technology we will refine is generally applicable to ASO drug development. Therefore, this research has the potential to turn tide on the battlefield against COVID-19 and in our fight with many other diseases.