The blockade of immune checkpoints, such as programmed death receptor 1 (PD-1) and programmed death ligand 1 protein (PD-L1), is a promising therapeutic approach in cancer immunotherapy. Nivolumab, a humanized IgG4 antibody targeting PD-1, was approved by the US Food and Drug Administration for several cancers in 2014. Crystal structures of the nivolumab/PD-1 complex show that the epitope of PD-1 locates at the IgV domain (including the FG and BC loops) and the N-terminal loop. Although the N-terminal loop of PD-1 has been shown to play a dominant role in the complex interface of the static structure, its role in the dynamic binding process has not been illustrated clearly. Here, eight molecular systems were established for nivolumab/PD-1 complex, and long-time molecular dynamics simulations were performed for each. Results showed that the N-terminal loop of PD-1 prefers to bind with nivolumab to stabilize the interface between IgV and nivolumab. Furthermore, the binding of the N-terminal loop with nivolumab induces the rebinding between the IgV domain and nivolumab. Thus, we proposed a two-step binding model for the nivolumab/PD-1 binding, where the interface switches to a high-affinity state with the help of the N-terminal loop. This finding suggests that the N-terminal loop of PD-1 might be a potential target for anti-PD-1 antibody design, which could serve as an important gatekeeper for the anti-PD-1 antibody binding.

诸如程序性死亡受体1（PD-1）和程序性死亡配体1蛋白（PD-L1）等免疫检查点的封锁是癌症免疫疗法中一种有希望的治疗方法。Nivolumab是一种针对PD-1的人源化IgG4抗体，已于2014年获得美国食品和药物管理局的批准，可用于多种癌症。nivolumab / PD-1复合物的晶体结构表明PD-1的表位位于IgV结构域（包括FG和BC回路）和N端回路。尽管已经表明PD-1的N末端环在静态结构的复杂界面中起主要作用，但是其在动态结合过程中的作用尚未清楚地说明。在这里，为nivolumab / PD-1复合物建立了八个分子系统，并对每个分子进行了长时间的分子动力学模拟。结果表明，PD-1的N末端环更喜欢与nivolumab结合，以稳定IgV和nivolumab之间的界面。此外，N末端环与nivolumab的结合诱导了IgV结构域和nivolumab之间的重新结合。因此，我们提出了针对nivolumab / PD-1结合的两步结合模型，其中，在N端环的帮助下，界面切换至高亲和力状态。这一发现表明，PD-1的N末端环可能是抗PD-1抗体设计的潜在靶标，可以作为抗PD-1抗体结合的重要看门人。我们为nivolumab / PD-1结合提出了两步结合模型，其中，在N末端环的帮助下，界面切换为高亲和力状态。这一发现表明，PD-1的N末端环可能是抗PD-1抗体设计的潜在靶标，可以作为抗PD-1抗体结合的重要看门人。我们为nivolumab / PD-1结合提出了两步结合模型，其中，在N末端环的帮助下，界面切换为高亲和力状态。这一发现表明，PD-1的N末端环可能是抗PD-1抗体设计的潜在靶标，可以作为抗PD-1抗体结合的重要看门人。