Remesh Soumya G, Merz Gregory E, Brilot Axel F, Chio Un Seng, Rizo Alexandrea N, Pospiech Thomas H, Lui Irene, Laurie Mathew T, Glasgow Jeff, Le Chau Q, Zhang Yun, Diwanji Devan, Hernandez Evelyn, Lopez Jocelyne, Pawar Komal Ishwar, Pourmal Sergei, Smith Amber M, Zhou Fengbo, DeRisi Joseph, Kortemme Tanja, Rosenberg Oren S, Glasgow Anum, Leung Kevin K, Wells James A, Verba Kliment A
Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA - 94158, USA.
QBI Coronavirus Research Group Structural Biology Consortium, University of California, San Francisco, CA - 94158, USA.
bioRxiv. 2022 Aug 10:2022.08.09.503400. doi: 10.1101/2022.08.09.503400.
The SARS-CoV-2 Omicron variant, with 15 mutations in Spike receptor binding domain (Spike-RBD), renders virtually all clinical monoclonal antibodies against WT SARS-CoV-2 ineffective. We recently engineered the SARS-CoV-2 host entry receptor, ACE2, to tightly bind WT-Spike-RBD and prevent viral entry into host cells ("receptor traps"). Here we determine cryo-EM structures of our receptor traps in complex with full length Spike. We develop a multi-model pipeline combining Rosetta protein modeling software and cryo-EM to allow interface energy calculations even at limited resolution and identify interface side chains that allow for high affinity interactions between our ACE2 receptor traps and Spike-RBD. Our structural analysis provides a mechanistic rationale for the high affinity (0.53 - 4.2nM) binding of our ACE2 receptor traps to Omicron-RBD confirmed with biolayer interferometry measurements. Finally, we show that ACE2 receptor traps potently neutralize Omicron- and Delta-pseudotyped viruses, providing alternative therapeutic routes to combat this evolving virus.
严重急性呼吸综合征冠状病毒2（SARS-CoV-2）的奥密克戎变种在刺突受体结合域（Spike-RBD）有15个突变，几乎使所有针对野生型SARS-CoV-2的临床单克隆抗体失效。我们最近对SARS-CoV-2的宿主进入受体血管紧张素转换酶2（ACE2）进行了改造，使其紧密结合野生型Spike-RBD并阻止病毒进入宿主细胞（“受体陷阱”）。在此，我们确定了我们的受体陷阱与全长刺突蛋白复合物的冷冻电镜结构。我们开发了一个结合Rosetta蛋白质建模软件和冷冻电镜的多模型流程，即使在有限分辨率下也能进行界面能量计算，并识别出允许我们的ACE2受体陷阱与Spike-RBD之间进行高亲和力相互作用的界面侧链。我们的结构分析为我们的ACE2受体陷阱与奥密克戎-RBD的高亲和力（0.53 - 4.2nM）结合提供了机制依据，这一结合通过生物层干涉测量得到了证实。最后我们表明，ACE2受体陷阱能有效中和奥密克戎和德尔塔假型病毒，为对抗这种不断演变的病毒提供了替代治疗途径。
