Targeting early metastable intermediates of the SARS-CoV-2 spike for vaccine and therapeutics development

新型SARS-CoV-2冠状病毒（CoV）正在全球流行，迫切需要开发有效的预防和治疗方法。病毒-宿主细胞融合(S)蛋白突刺由于其在病毒生命周期中的关键作用而成为此类治疗的主要目标。S蛋白分为两个区域：n端S1结构域覆盖c端S2融合结构域。通过S1中的受体结合域（RBD）与宿主受体结合，随后宿主蛋白酶对刺突进行蛋白水解裂解。这导致了剧烈的构象转变，导致S1脱落和S2中的融合机制暴露，最终导致宿主细胞进入。一类融合蛋白，如冠状病毒S蛋白，在融合过程中发生了很大的构象变化，必须具有高度的灵活性和动态性。事实上，SARS-CoV-2突刺的低温电镜结构在S1结构域显示出相当大的灵活性和动力学，特别是在RBD周围，RBD表现出两种离散的构象状态——屏蔽受体结合的“下”状态和受体可接近的“上”状态。本研究的总体目标是使用我们强大的，高通量的计算和实验管道来定义详细的轨迹

TThe ongoing global pandemic of the novel SARS-CoV-2 coronavirus (CoV) presents an urgent need for development of effective preventative and treatment therapies. The viral-host cell fusion (S) protein spike is a prime target for such therapies owing to its critical role in the virus lifecycle. The S protein is divided into two regions: the N-terminal S1 domain that caps the C-terminal S2 fusion domain. Binding to host receptor via the Receptor Binding Domain (RBD) in S1 is followed by proteolytic cleavage of the spike by host proteases. This leads dramatic conformational transitions resulting in S1 shedding and exposure of the fusion machinery in S2, culminating in host-cell entry. Class I fusion proteins such as the CoV S protein that undergo large conformational changes during the fusion process must, by necessity, be highly flexible and dynamic. Indeed, cryo-EM structures of the SARS-CoV-2 spike reveal considerable flexibility and dynamics in the S1 domain, especially around the RBD that exhibits two discrete conformational states – a “down” state that is shielded from receptor binding, and an “up” state that is receptor-accessible. The overall goals of this study are to use our robust, high-throughput computational and experimental pipeline to define the detailed trajectory of the “down” to “up” transition of the SARS-CoV-2 S protein, identify early metastable intermediates in the fusion pathway, and exploit their structures and dynamics for identifying drug and vaccine candidates that target SARS-CoV-2. A wealth of structural information on CoV spike proteins, including recently determined cryo-EM structures of the SARS-CoV-2 spike, provides a rich source of detailed data from which to begin precise examination of macromolecular transitions underlying triggering of this fusion machine