Guo Liyan, Chen Zimin, Lin Sheng, Yang Fanli, Yang Jing, Wang Lingling, Zhang Xindan, Yuan Xin, He Bin, Cao Yu, Li Jian, Zhao Qi, Lu Guangwen
Department of Emergency Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
Department of Hematology, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
PLoS Pathog. 2025 Apr 11;21(4):e1013034. doi: 10.1371/journal.ppat.1013034. eCollection 2025 Apr.
The persistent emergence of new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants highlights the need for developing broad-spectrum antiviral agents. Here, we report the identification of two sarbecovirus S2-specific alpaca nanobodies, namely H17 and H145, that effectively neutralize known SARS-CoV-2 variants (including the Omicron subvariants) and other sarbecoviruses (such as SARS-CoV, PANG/GD, WIV1, and HKU3). The two nanobodies recognize a linear epitope (D1139PLQPELDSFKEEL1152) in the upper region of the S2 stem-helix (SH), which is highly conserved among SARS-CoV-2 variants and other sarbecoviruses. The complex structure of the nanobody bound to the epitope SH-peptide reveal that nanobody binding will impede the refolding of S2, effectively neutralizing the virus. Moreover, the nanobodies bind viral S2 in an acidification-insensitive manner, demonstrating their capacity for entry inhibition especially when viruses enter via the endosomal route. Finally, H17 and H145 possess a better taking-action window for virus neutralization, superior to the RBD-targeting nanobodies that exert neutralization by competing against ACE2 binding. Taken together, the results suggest that anti-SH nanobodies H17 and H145 are promising broad-spectrum drug candidates for preventing and treating the pandemic infections by SARS-CoV-2 variants and other sarbecoviruses.
新型严重急性呼吸综合征冠状病毒2（SARS-CoV-2）变种的持续出现凸显了开发广谱抗病毒药物的必要性。在此，我们报告鉴定出两种沙贝病毒S2特异性羊驼纳米抗体，即H17和H145，它们可有效中和已知的SARS-CoV-2变种（包括奥密克戎亚变种）及其他沙贝病毒（如SARS-CoV、PANG/GD、WIV1和HKU3）。这两种纳米抗体识别S2茎螺旋（SH）上部区域的一个线性表位（D1139PLQPELDSFKEEL1152），该表位在SARS-CoV-2变种和其他沙贝病毒中高度保守。纳米抗体与表位SH肽结合的复合物结构显示，纳米抗体的结合会阻碍S2的重折叠，从而有效中和病毒。此外，纳米抗体以对酸化不敏感的方式结合病毒S2，表明它们具有抑制病毒进入的能力，尤其是当病毒通过内体途径进入时。最后，H17和H145在病毒中和方面具有更好的作用窗口，优于通过竞争ACE2结合发挥中和作用的靶向RBD的纳米抗体。综上所述，结果表明抗SH纳米抗体H17和H145是预防和治疗SARS-CoV-2变种及其他沙贝病毒大流行感染的有前景的广谱药物候选物。
