Li Shiliang, Ye Fang, Zheng Yucheng, Wang Jie, Peng Haoran, Zhu Lili, Chen Lili, Yu Tao, Ge Huan, He Jiaqi, Zhang Binghao, Wu Jiayun, Zhang Zhiyi, Jiang Liangliang, Chen Geng, Zhao Ping, Lan Ke, Zhao Zhenjiang, Qian Xuhong, Xu Ke, Du Yang, Li Honglin
Innovation Center for AI and Drug Discovery, School of Pharmacy, East China Normal University, Shanghai, 200062, China.
Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science & Technology, Shanghai, 200237, China.
Adv Sci (Weinh). 2025 Jul;12(27):e2417534. doi: 10.1002/advs.202417534. Epub 2025 Apr 26.
The SARS-CoV-2 spike (S) protein, a trimeric structure comprising three receptor binding domains (RBDs) and three N-terminal domains (NTDs), undergoes substantial conformational changes to a fusion-prone open state for angiotensin-converting enzyme 2 (ACE2) binding and host cell infection. Stabilizing its closed state is a key antiviral strategy but remains challenging. Here, we introduce S416, a novel amphipathic molecule acting as a "molecular bolt". Cryo-EM study reveals that S416 binds concurrently to six sites across two distinct druggable interfaces: three molecules at the RBD-RBD interfaces and three at the NTD-RBD interfaces. This unique "dual-locking" mechanism, driven by S416's polar carboxyl head and nonpolar phenylthiazole tail, robustly stabilizes the spike trimer in a locked, closed conformation through strong inter-domain interactions, reducing structural flexibility and atomic fluctuations compared to the apo structure resolved synchronously. Crucially, these RBD-RBD and NTD-RBD interfaces are conserved across human-infecting coronaviruses, suggesting potential as broad-spectrum antiviral targets. Our findings demonstrate that the highly dynamic spike trimer can be effectively stabilized by an amphipathic molecular bolt targeting both the inter- and intra-monomer interfaces, offering a promising strategy against emerging coronaviruses.
严重急性呼吸综合征冠状病毒2（SARS-CoV-2）刺突（S）蛋白是一种三聚体结构，由三个受体结合结构域（RBD）和三个N端结构域（NTD）组成，会发生显著的构象变化，转变为易于融合的开放状态，以结合血管紧张素转换酶2（ACE2）并感染宿主细胞。稳定其封闭状态是一种关键的抗病毒策略，但仍然具有挑战性。在此，我们引入了S416，一种新型的两亲性分子，起到“分子螺栓”的作用。冷冻电镜研究表明，S416同时结合两个不同的可成药界面上的六个位点：三个分子位于RBD-RBD界面，三个位于NTD-RBD界面。这种独特的“双重锁定”机制由S416的极性羧基头部和非极性苯基噻唑尾部驱动，通过强大的结构域间相互作用，有力地将刺突三聚体稳定在锁定的封闭构象中，与同步解析的无配体结构相比，降低了结构灵活性和原子波动。至关重要的是，这些RBD-RBD和NTD-RBD界面在感染人类的冠状病毒中是保守的，表明其作为广谱抗病毒靶点的潜力。我们的研究结果表明，高度动态的刺突三聚体可以通过靶向单体间和单体内界面的两亲性分子螺栓有效地稳定下来，为对抗新兴冠状病毒提供了一种有前景的策略。
