通过计算设计和合成文库筛选获得广谱沙贝科病毒中和抗体。
Broad Sarbecovirus Neutralizing Antibodies Obtained by Computational Design and Synthetic Library Screening.
机构信息
NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
出版信息
J Virol. 2023 Jul 27;97(7):e0061023. doi: 10.1128/jvi.00610-23. Epub 2023 Jun 27.
Members of the subgenus of have twice caused deadly threats to humans. There is increasing concern about the rapid mutation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which has evolved into multiple generations of epidemic variants in 3 years. Broad neutralizing antibodies are of great importance for pandemic preparedness against SARS-CoV-2 variants and divergent zoonotic sarbecoviruses. Here, we analyzed the structural conservation of the receptor-binding domain (RBD) from representative sarbecoviruses and chose S2H97, a previously reported RBD antibody with ideal breadth and resistance to escape, as a template for computational design to enhance the neutralization activity and spectrum. A total of 35 designs were purified for evaluation. The neutralizing activity of a large proportion of these designs against multiple variants was increased from several to hundreds of times. Molecular dynamics simulation suggested that extra interface contacts and enhanced intermolecular interactions between the RBD and the designed antibodies are established. After light and heavy chain reconstitution, AI-1028, with five complementarity determining regions optimized, showed the best neutralizing activity across all tested sarbecoviruses, including SARS-CoV, multiple SARS-CoV-2 variants, and bat-derived viruses. AI-1028 recognized the same cryptic RBD epitope as the parental prototype antibody. In addition to computational design, chemically synthesized nanobody libraries are also a precious resource for rapid antibody development. By applying distinct RBDs as baits for reciprocal screening, we identified two novel nanobodies with broad activities. These findings provide potential pan-sarbecovirus neutralizing drugs and highlight new pathways to rapidly optimize therapeutic candidates when novel SARS-CoV-2 escape variants or new zoonotic coronaviruses emerge. The subgenus includes human SARS-CoV, SARS-CoV-2, and hundreds of genetically related bat viruses. The continuous evolution of SARS-CoV-2 has led to the striking evasion of neutralizing antibody (NAb) drugs and convalescent plasma. Antibodies with broad activity across sarbecoviruses would be helpful to combat current SARS-CoV-2 mutations and longer term animal virus spillovers. The study of pan-sarbecovirus NAbs described here is significant for the following reasons. First, we established a structure-based computational pipeline to design and optimize NAbs to obtain more potent and broader neutralizing activity across multiple sarbecoviruses. Second, we screened and identified nanobodies from a highly diversified synthetic library with a broad neutralizing spectrum using an elaborate screening strategy. These methodologies provide guidance for the rapid development of antibody therapeutics against emerging pathogens with highly variable characteristics.
属的亚属成员两次对人类造成致命威胁。人们越来越关注严重急性呼吸综合征冠状病毒 2(SARS-CoV-2)的快速突变,该病毒在 3 年内已经进化成多代流行变种。广谱中和抗体对于 SARS-CoV-2 变种和不同宿主来源的沙贝冠状病毒的大流行防范至关重要。在这里,我们分析了代表性沙贝冠状病毒的受体结合域(RBD)的结构保守性,并选择了先前报道的具有理想广度和逃逸抗性的 RBD 抗体 S2H97 作为计算设计模板,以增强中和活性和广谱性。总共纯化了 35 个设计进行评估。这些设计中的很大一部分对多种变体的中和活性提高了几个数量级到数百倍。分子动力学模拟表明,RBD 与设计抗体之间建立了额外的界面接触和增强的分子间相互作用。重链和轻链重建后,经过五个互补决定区优化的 AI-1028 在所有测试的沙贝冠状病毒中表现出最佳的中和活性,包括 SARS-CoV、多种 SARS-CoV-2 变体和源自蝙蝠的病毒。AI-1028 识别与亲本原型抗体相同的隐蔽 RBD 表位。除了计算设计外,化学合成的纳米抗体文库也是快速开发抗体的宝贵资源。通过将不同的 RBD 作为相互筛选的诱饵应用,我们鉴定了两种具有广泛活性的新型纳米抗体。这些发现为泛沙贝冠状病毒中和药物提供了潜在的候选药物,并突出了当出现新的 SARS-CoV-2 逃逸变体或新的动物冠状病毒时,快速优化治疗候选药物的新途径。 亚属包括人类 SARS-CoV、SARS-CoV-2 和数百种遗传上相关的蝙蝠病毒。SARS-CoV-2 的持续进化导致中和抗体(NAb)药物和恢复期血浆的显著逃逸。具有广谱活性的抗体将有助于对抗当前的 SARS-CoV-2 突变和更长期的动物病毒溢出。这里描述的泛沙贝冠状病毒 NAb 研究具有以下意义。首先,我们建立了一个基于结构的计算管道,用于设计和优化 NAb,以获得对多种沙贝冠状病毒更有效和更广泛的中和活性。其次,我们使用精心设计的筛选策略,从高度多样化的合成文库中筛选和鉴定出具有广谱中和活性的纳米抗体。这些方法为快速开发针对具有高度可变特征的新兴病原体的抗体疗法提供了指导。