Comprehensive profiling of SARS-CoV-2 antibody responses and escape pathways

新型SARS-CoV-2冠状病毒（CoV）的持续全球大流行迫切需要开发有效的预防和治疗疗法。病毒-宿主细胞融合（S）蛋白刺突由于其在病毒生命周期中的关键作用而成为此类疗法的主要靶标。S蛋白分为两个区域：N-末端S1结构域覆盖C-末端S2融合结构域。通过S1中的受体结合结构域（RBD）与宿主受体结合，随后通过宿主蛋白酶对刺突进行蛋白水解切割。这导致了戏剧性的构象转变，导致S1脱落和S2中融合机制的暴露，最终进入宿主细胞。I类融合蛋白，如在融合过程中经历大的构象变化的CoV S蛋白，必须是高度灵活和动态的。事实上，SARS-CoV-2刺突的cryo-EM结构在S1结构域中显示出相当大的灵活性和动态性，特别是在RBD周围，其表现出两种离散的构象状态-“向下”状态，其被屏蔽而不与受体结合，而“向上”状态是受体可接近的。这项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， SARS-CoV-2 S蛋白的“向下”到“向上”转变，鉴定融合途径中的早期亚稳态中间体，并利用它们的结构和动力学来鉴定靶向SARS-CoV-2的候选药物和疫苗。CoV刺突蛋白的丰富结构信息，包括最近确定的SARS-CoV-2刺突的cryo-EM结构，提供了丰富的详细数据来源，从中开始精确检查触发这种融合机器的大分子转变。本研究的科学前提是，了解SARS-CoV-2刺突移动的区域的结构动力学和早期转变动力学将允许疫苗和药物反应的最佳控制，并促进新型抗病毒药物和保护性疫苗的开发。在这项研究的高潮，我们希望有确定的结构的多个“下”，“上”，和中间状态的SARS-CoV-2 S蛋白。总之，这些研究将提供重要的原子详细的结构和机制的信息，用于开发疫苗和治疗设计。

The 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. The scientific premise of this study is that understanding the structural dynamics and early transition kinetics of mobile regions of the SARS-CoV-2 spike will allow optimal control of vaccine and drug responses, and facilitate the development of novel antiviral drugs and protective vaccines. At the culmination of this study, we expect to have determined structures of multiple “down”, “up”, and intermediate states of the SARS-CoV-2 S protein. Together, these studies will provide important atomically detailed structural and mechanistic information for exploitation in vaccine and therapeutics design.