De Novo Design of Minibinder Antagonists for COVID-19 and Future Pandemics

项目总结 新冠肺炎大流行最紧迫的公共卫生优先事项之一是制定有效的 而且便宜的治疗方法。这项提议的长期目标是开发诸如以下新冠肺炎疗法 以及一旦发现任何新的病原体就迅速创建此类分子所需的方法。这个 中心假设是，计算设计可以用来快速制造出具有强大抗病毒活性的蛋白质 以及其他抑制与晚期感染相关的“细胞因子风暴”的药物。这种反制措施，如果迅速 开发和部署，可以在暴发期间拯救数百万人的生命，直到疫苗被开发出来。这个 具体目标是：1)通过以下方式克服目前蛋白质疗法发现和发展中的限制 创造与脆弱结合位点紧密结合的超稳定微型蛋白的从头设计方法 SARS-CoV-2刺突糖蛋白，包括ACE-2细胞的受体结合域 2)通过基因工程提高抗钉钉小分子的亲和力。 多个拷贝的融合，或者通过合理设计更高阶的低聚物来产生药物化合物 不太容易发生病毒突变逃逸；3)应用相同的迷你粘合剂设计流水线来创建细胞因子受体 关键细胞因子IL-6和IL-1β拮抗剂可能参与急性呼吸窘迫综合征(ADRS) 与新冠肺炎死亡率有关；4)通过以下几项评估抗病毒和抗白细胞介素型迷你粘合剂的疗效 新冠肺炎啮齿动物模型的静脉、鼻腔和皮下给药途径及评价 免疫原性，以确定最适合进一步临床前开发的设计。作为证明 原理上，第一个抗钉病毒的小粘合剂已经设计出来，被发现可以与SARS-CoV-2钉结合 RBD，并被发现中和活病毒的活性与最有效的已知抗体相媲美。这 提案具有创新性，因为它寻求在新的计算设计中应用强大的新兴方法 新冠肺炎大流行的蛋白质疗法。这项提议意义重大，因为它将是第一个例子 计算蛋白质设计产生有效的和完全从头开始的抗病毒和抗炎疗法 应对一场活跃的大流行。最终，快速迷你粘结剂设计方法有可能产生治疗方法 对于未来的大流行，以及许多其他常见和被忽视的疾病和情况。

PROJECT SUMMARY One of the most pressing public health priorities for the COVID-19 pandemic is the development of an effective and inexpensive therapeutic. The long-term goal of this proposal is to develop such COVID-19 treatments, as well as the methods needed to rapidly create such molecules as soon as any new pathogen is identified. The central hypothesis is that computational design can be used to quickly create proteins with potent antiviral activity and others that suppress “cytokine storms” associated with advanced infection. Such countermeasures, if rapidly developed and deployed, could save millions of lives during an outbreak until vaccines are developed. The specific aims are to: 1) overcome current limitations in the discovery and development of protein therapeutics by creating methods for the de novo design of hyper-stable miniproteins that bind tightly to vulnerable binding sites on the SARS-CoV-2 Spike glycoprotein, including the receptor binding domain (RBD) of the ACE-2 cellular receptor and the fusion peptide region; 2) Enhance the avidity of such anti-Spike minibinders through genetic fusion of multiple copies, or through rational design of higher-order oligomers to create drug compounds that are less prone to viral mutagenic escape; 3) Apply the same minibinder design pipeline to create cytokine receptor antagonists of key cytokines IL-6 and IL-1β likely involved in acute respiratory distress syndrome (ADRS) associated with COVID-19 mortality; 4) Assess the efficacy of antiviral and anti-interleukin minibinders by several routes of delivery (intravenous, intranasal and subcutaneous) in rodent models of COVID-19 and assess immunogenicity in order to identify those designs best suited for further preclinical development. As proof of principle, the first anti-Spike minibinders have already been designed, were found to bind to SARS-CoV-2 Spike RBD, and were found to neutralize live virus with activities rivaling the most potent known antibodies. This proposal is innovative because it seeks to apply powerful emerging methods in the computational design of new protein therapeutics to the COVID-19 pandemic. The proposal is significant because it would be the first example of computational protein design yielding potent and entirely de novo antiviral and anti-inflammatory therapeutics for an active pandemic. Ultimately, rapid minibinder design methods have the potential to generate treatments for future pandemics, as well as for many other common and neglected diseases and conditions.