Investigating the Role of the N-Terminal Loop of PD-1 in Binding Process Between PD-1 and Nivolumab via Molecular Dynamics Simulation

Abstract

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.

Keywords: N-terminal loop; PD-1; molecular dynamics simulation; nivolumab; two-step model.

FIGURE 1

Eight molecular systems of nivolumab/PD-1 complex. (A) Complex I. It is downloaded from the PDB with accession code of 5GGR. (B) Complex I-N-truncated. It is built through cutting off the N-terminal loop of PD-1 of Complex I. (C) Complex I-N-rotated. It is built through the rotation of the N-terminal loop of PD-1 of Complex I. (D) Complex I-IgV-rotated. It is built through the rotation of the IgV domain of PD-1 of Complex I. (E) Complex II. It is downloaded from the PDB with accession code of 5WT9. (F) Complex II-N-truncated. It is built through cutting off the N-terminal loop of PD-1 of Complex II. (G) Complex II-N-rotated. It is built through the rotation of the N-terminal loop of PD-1 of complex II. (H) Complex II-IgV-rotated. It is built through the rotation of the IgV domain of PD-1 of Complex II. The nivolumab is shown in silver (Surface mode). The N-terminal loop of PD-1 is shown in blue (New Cartoon mode). The FG loop and the BC loop of the IgV domain are shown in red, and the rest parts of the IgV domain are shown in yellow (New Cartoon mode).

FIGURE 2

Buried SASA (A), interaction energy (B), and number of H-bonds (C) of Complex I in three runs (Equ1, Equ2, and Equ3). (D–F) Show the last frame of Complex I in Equ1, Equ2, and Equ3, respectively. The nivolumab is shown in silver (Surface mode). The N-terminal loop of PD-1 is shown in blue and the IgV domain of PD-1 is shown in yellow (New Cartoon mode). The interaction residues of PD-1 are shown in red (Licorice mode).

FIGURE 3

Buried SASA (A), interaction energy (B), and number of H-bonds (C) of Complex II in three runs (Equ1, Equ2, and Equ3). (D–F) Show the last frame of Complex II in Equ1, Equ2, and Equ3, respectively. The nivolumab is shown in silver (Surface mode). The N-terminal loop of PD-1 is shown in blue and the IgV domain of PD-1 is shown in yellow (New Cartoon mode). The interaction residues of PD-1 are shown in red (Licorice mode).

FIGURE 4

(A–C) Demonstrate distributions of buried SASA, interaction energy, and number of H-bonds for Complex I, Complex I-N-truncated, Complex I-N-rotated, and Complex I-IgV-rotated. (D–F) Demonstrate distributions of buried SASA, interaction energy, and number of H-bonds for Complex II, Complex II-N-truncated, Complex II-N-rotated, and Complex II-IgV-rotated.

FIGURE 5

Buried SASA (A), interaction energy (B), and number of H-bonds (C) of Complex I-N-truncated in three runs (Equ1, Equ2, and Equ3). (D–F) Show the last frame of Complex I-N-truncated in Equ1, Equ2, and Equ3, respectively. The IgV domain of PD-1 is shown in yellow (New Cartoon mode). The interaction residues of PD-1 are shown in red (Licorice mode).

FIGURE 6

Buried SASA (A), interaction energy (B), and number of H-bonds (C) of Complex II-N-truncated in three runs (Equ1, Equ2, and Equ3). (D–F) Show the last frame of Complex II-N-truncated in Equ1, Equ2, and Equ3, respectively. The IgV domain of PD-1 is shown in yellow (New Cartoon mode). The interaction residues of PD-1 are shown in red (Licorice mode).

FIGURE 7

Number of water molecules within 4 Å of the BC (A) and FG (B) loops of Complex I, Complex I-N-truncated, Complex II and Complex II-N-truncated in three runs. *p < 0.05, **p < 0.01.

FIGURE 8

Buried SASA (A), interaction energy (B), and number of H-bonds (C) of Complex I-N-rotated in three runs (Equ1, Equ2, and Equ3). (D,E) Show the number of H-bonds formed by the N-terminal loop and the IgV domain of PD-1, respectively. (F) shows the RMSD of the N-terminal loop of PD-1 of Complex I-N-rotated in relative to its initial conformation in Complex I in three runs. (G–I) Show the last frame of Complex I-N-rotated in Equ1, Equ2, and Equ3, respectively. The N-terminal loop of PD-1 is shown in blue and the IgV domain of PD-1 is shown in yellow (New Cartoon mode). The interaction residues of PD-1 are shown in red (Licorice mode).

FIGURE 9

Buried SASA (A), interaction energy (B), and number of H-bonds (C) of Complex II-N-rotated in three runs (Equ1, Equ2, and Equ3). (D,E) Show the number of H-bonds formed by the N-terminal loop and the IgV domain of PD-1, respectively. (F) Shows the RMSD of the N-terminal loop of PD-1 of Complex II-N-rotated in relative to its initial conformation in Complex II in three runs. (G–I) Show the last frame of Complex II-N-rotated in Equ1, Equ2, and Equ3, respectively. The N-terminal loop of PD-1 is shown in blue and the IgV domain of PD-1 is shown in yellow (New Cartoon mode). The interaction residues of PD-1 are shown in red (Licorice mode).

FIGURE 10

Buried SASA (A), interaction energy (B), and number of H-bonds (C) of Complex I-IgV-rotated in three runs (Equ1, Equ2, and Equ3). (D,E) Show the number of H-bonds formed by the N-terminal loop and the IgV domain of PD-1, respectively. (F) Shows the RMSD of the IgV domain of PD-1 of Complex I-IgV-rotated in relative to its initial conformation in Complex I in three runs. (G–I) Show the last frame of Complex I-IgV-rotated in Equ1, Equ2, and Equ3, respectively. The N-terminal loop of PD-1 is shown in blue and the IgV domain of PD-1 is shown in yellow (New Cartoon mode). The interaction residues of PD-1 are shown in red (Licorice mode).

FIGURE 11

Buried SASA (A), interaction energy (B), and number of H-bonds (C) of Complex II-IgV-rotated in three runs (Equ1, Equ2, and Equ3). (D,E) Show the number of H-bonds formed by the N-terminal loop and the IgV domain of PD-1, respectively. (F) Shows the RMSD of the IgV domain of PD-1 of Complex II-IgV-rotated in relative to its initial conformation in Complex II in three runs. (G–I) Show the last frame of Complex II-IgV-rotated in Equ1, Equ2, and Equ3, respectively. The N-terminal loop of PD-1 is shown in blue and the IgV domain of PD-1 is shown in yellow (New Cartoon mode). The interaction residues of PD-1 are shown in red (Licorice mode).