Fu Ying, Rezende E Mello Juliana da Fonseca, Fleming Bryan D, Renn Alex, Chen Catherine Z, Hu Xin, Xu Miao, Gorshkov Kirill, Hanson Quinlin, Zheng Wei, Lee Emily M, Perera Lalith, Petrovich Robert, Pradhan Manisha, Eastman Richard T, Itkin Zina, Stanley Thomas, Hsu Allen, Dandey Venkata, Gillette William, Taylor Troy, Ramakrishnan Nitya, Perkins Shelley, Esposito Dominic, Oh Eunkeu, Susumu Kimihiro, Wolak Mason, Ferrer Marc, Hall Matthew D, Borgnia Mario J, Simeonov Anton
bioRxiv. 2022 Mar 1:2021.10.22.465476. doi: 10.1101/2021.10.22.465476.
Neutralizing antibodies targeting the SARS-CoV-2 spike protein have shown a great preventative/therapeutic potential. Here, we report a rapid and efficient strategy for the development and design of SARS-CoV-2 neutralizing humanized nanobody constructs with sub-nanomolar affinities and nanomolar potencies. CryoEM-based structural analysis of the nanobodies in complex with spike revealed two distinct binding modes. The most potent nanobody, RBD-1-2G(NCATS-BL8125), tolerates the N501Y RBD mutation and remains capable of neutralizing the B.1.1.7 (Alpha) variant. Molecular dynamics simulations provide a structural basis for understanding the neutralization process of nanobodies exclusively focused on the spike-ACE2 interface with and without the N501Y mutation on RBD. A primary human airway air-lung interface (ALI) model showed that RBD-1-2G-Fc antibody treatment was effective at reducing viral burden following WA1 and B.1.1.7 SARS-CoV-2 infections. Therefore, this presented strategy will serve as a tool to mitigate the threat of emerging SARS-CoV-2 variants.
靶向严重急性呼吸综合征冠状病毒2（SARS-CoV-2）刺突蛋白的中和抗体已显示出巨大的预防/治疗潜力。在此，我们报告了一种快速有效的策略，用于开发和设计具有亚纳摩尔亲和力和纳摩尔效力的SARS-CoV-2中和人源化纳米抗体构建体。基于冷冻电镜的纳米抗体与刺突复合物的结构分析揭示了两种不同的结合模式。最有效的纳米抗体RBD-1-2G（NCATS-BL8125）能够耐受N501Y RBD突变，并仍然能够中和B.1.1.7（Alpha）变体。分子动力学模拟为理解纳米抗体的中和过程提供了结构基础，该过程专门针对RBD上有无N501Y突变的刺突-血管紧张素转换酶2（ACE2）界面。原代人气道气-肺界面（ALI）模型表明，RBD-1-2G-Fc抗体治疗在降低WA1和B.1.1.7 SARS-CoV-2感染后的病毒载量方面是有效的。因此，本文提出的策略将作为一种工具来减轻新出现的SARS-CoV-2变体的威胁。
