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

项目摘要 针对COVID-19大流行，最紧迫的公共卫生优先事项之一是制定有效的 和廉价的治疗。该提案的长期目标是开发COVID-19治疗方法， 以及一旦发现任何新的病原体就迅速产生这种分子所需的方法。的 核心假设是，计算机设计可以用来快速创建具有有效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。如果迅速采取此类对策， 开发和部署，可以在疫情爆发期间挽救数百万人的生命，直到疫苗开发出来。的 具体的目的是：1）克服目前在发现和开发蛋白质治疗剂方面的限制， 创造了从头设计超稳定微蛋白的方法，这些微蛋白紧密地结合到脆弱的结合位点上， SARS-CoV-2刺突糖蛋白，包括ACE-2细胞的受体结合结构域（RBD）， 2）通过遗传修饰增强这种抗刺突微小结合物的亲合力; 多个拷贝的融合，或通过合理设计更高级的寡聚体来产生药物化合物， 更不易于病毒致突变逃逸; 3）应用相同的微结合剂设计管道来产生细胞因子受体 可能参与急性呼吸窘迫综合征（ADRS）的关键细胞因子IL-6和IL-1β的拮抗剂 与COVID-19死亡率相关; 4）通过几种方法评估抗病毒和抗白细胞介素微结合剂的疗效 给药途径（静脉内、鼻内和皮下），并评估 免疫原性，以鉴定最适合进一步临床前开发的那些设计。就证明了 根据这一原理，已经设计出了第一批抗刺突蛋白的微型结合物，发现它们与SARS-CoV-2刺突蛋白结合。 RBD，并发现中和活病毒的活动相媲美的最有效的已知抗体。这 该提案是创新的，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 计算蛋白质设计产生有效的和完全从头抗病毒和抗炎治疗 一场活跃的流行病。最终，快速的微粘结剂设计方法有可能产生处理方法， 对于未来的流行病，以及许多其他常见和被忽视的疾病和条件。

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.