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

SARS-CoV-2 抗体反应和逃逸途径的综合分析

基本信息

批准号：
10265760
负责人：
JULIE M. OVERBAUGH
金额：
$ 48.97万
依托单位：
FRED HUTCHINSON CANCER RESEARCH CENTER
依托单位国家：
美国
项目类别：
财政年份：
2020
资助国家：
美国
起止时间：
2020-06-01 至 2022-03-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10265760
关键词：
2019-nCoV Amino Acid Sequence Amino Acids Antibodies Antibody Response Antiviral Agents Bacteriophages Binding Biological Assay C-terminal COVID-19 Cell fusion Cells Chimeric Proteins Clinical Complement Coronavirus Coronavirus Infections Coronavirus spike protein Cryoelectron Microscopy Data Development Diagnostic Disease Ebola virus Epitopes Exhibits Genetic Genome Goals HIV HIV Antibodies Immune Immunoprecipitation Infection Kinetics Libraries Methods Middle East Respiratory Syndrome Molecular Conformation Monoclonal Antibodies Mutation N-terminal Outcome Pathogenesis Pathway interactions Peptide Hydrolases Peptide Library Peptides Phage Display Pharmaceutical Preparations Plasma Population Preventive treatment Process Proteins Resolution Role SARS-CoV-2 infection Sampling Severe Acute Respiratory Syndrome Source Structure Therapeutic Therapeutic antibodies Vaccine Design Vaccines Variant Viral Viral Proteins Virus Work conformational conversion convalescent plasma cross reactivity deep sequencing design drug candidate flexibility mutation screening neutralizing antibody novel pandemic disease protein aminoacid sequence rapid technique receptor receptor binding response vaccine candidate vaccine-induced antibodies

项目摘要

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.

新型SARS-CoV-2冠状病毒（CoV）正在全球大流行，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