Molecular dynamics of the immune checkpoint programmed cell death protein I, PD-1: conformational changes of the BC-loop upon binding of the ligand PD-L1 and the monoclonal antibody nivolumab

Abstract

Background: The immune checkpoint receptor programmed cell death protein I (PD-1) has been identified as a key target in immunotherapy. PD-1 reduces the risk of autoimmunity by inducing apoptosis in antigen-specific T cells upon interaction with programmed cell death protein ligand I (PD-L1). Various cancer types overexpress PD-L1 to evade the immune system by inducing apoptosis in tumor-specific CD8+ T cells. The clinically used blocking antibody nivolumab binds to PD-1 and inhibits the immunosuppressive interaction with PD-L1. Even though PD-1 is already used as a drug target, the exact mechanism of the receptor is still a matter of debate. For instance, it is hypothesized that the signal transduction is based on an active conformation of PD-1.

Results: Here we present the results of the first molecular dynamics simulations of PD-1 with a complete extracellular domain with a focus on the role of the BC-loop of PD-1 upon binding PD-L1 or nivolumab. We could demonstrate that the BC-loop can form three conformations. Nivolumab binds to the BC-loop according to the conformational selection model whereas PD-L1 induces allosterically a conformational change of the BC-loop.

Conclusion: Due to the structural differences of the BC-loop, a signal transduction based on active conformation cannot be ruled out. These findings will have an impact on drug design and will help to refine immunotherapy blocking antibodies.

Keywords: BC-loop; Mathematical oncology; Molecular dynamics; Nivolumab; PD-1; PD-L1.

Fig. 1

Binding partners influence flexibility of loops. The RMSF of C_αs of PD-1 unbound (black) and bound to either PD-L1 (red) or nivolumab (blue), when fitted to its respective first frame are shown. Whereas the impact of the binding partners on structured domains is negligible, the RMSF of the loops can change drastically. PD-1_Apo has the greatest flexibility except for the BC-loop. The fact that PD-L1 seems to induce more flexibility in the BC-loop led to detailed examination of the BC-loop

Fig. 2

PD-L1 induces a unique BC-loop conformation. The clustering algorithm as described by Daura et al. [20] was applied (a). Colors denote the origin of the structures. Only the first 25 clusters are shown. PD-1_PD-L1 (red) and PD-1_Niv (blue) exhibit for 25 and 60% of the time, respectively the same conformation. Over 90% of the structures of PD-1_Apo (black) are distributed between cluster 2 and 7. Cluster 3 and 5 contain only PD-1_PD-L1 structures whereas cluster 4 consist primarily PD-1_Niv structures. The number of structures is equivalent to the time the BC-loop resided in a certain conformation. b The distance map generated with multidimensional scaling [21] shows the relationship between the conformations found with the Daura et al. [20] clustering algorithm. Clusters with similar structures are in proximity. Three areas are distinguishable (circled by hand) which are named meta-cluster I, II and III. Meta-cluster I is occupied by the PD-1_Apo, PD-1_PD-L1 and PD-1_Niv. Meta-cluster II consists of clusters formed by PD-1_Apo. Meta-cluster III consists only of structures of PD-1_PD-L1. This demonstrates a clear shift of the BC-loop conformation in the Nivolumab complex. The colors represent the origins of the central frames. c Superimposed crystal structures of the central frames of the first five clusters visualized with VMD 1.9.3. Structures of clusters 1, 4 and 5 exhibit a similar BC-loop conformation. Cluster 2 and 3 exhibit distinct BC-loop conformations. BC-loop is colored; other domains are shown in grey. PD-1_Apo structure is shown in cyan instead of black

Fig. 3

Binding of PD-L1 and Nivolumab to PD-1. a Central member structure of cluster 3 of the BC-loop, binding to PD-L1; PD1- in grey, with the BC-loop in red sticks and PD-L1 in orange. b Central member structure of cluster 1 of the BC-loop, binding to Nivolumab; PD-1 in grey, with the BC-loop in blue sticks and Nivolumab in light blue. Hydrogen bonds between PD-1 and Nivolumab observed in this structure indicated in green. c, d zoomed in views of (a, b), respectively. PD-1 is in the same orientation in all four panels

Fig. 4

The BC-loop does not form any hydrogen bonds with PD-L1. a The frequencies of the number of hydrogen bonds formed between PD-1 and PD-L1 (red) and PD-1 and nivolumab (blue) over the course of 100 ns are shown. The PD-1 – PD-L1 complex has a peak of 17 formed hydrogen bonds which occur in 1400 frames (which corresponds to 14 ns). The PD-1 – Nivolumab complex formed 10 hydrogen bonds for 1500 frames. b Between the BC-loop and PD-L1 no hydrogen bonds are formed. The BC-loop and nivolumab form 2200 times 4 hydrogen bonds over the course of 100 ns. Also, for 2300 frames no hydrogen bond occurs between the BC-loop and nivolumab

Fig. 5

No non-bonded interactions between the BC-loop and PD-L1. a The non-bonded interaction energies between PD-1 and PD-L1 (red) and PD-1 and nivolumab (blue) are shown as a histogram and are grouped in packages of 100 kJ mol^− 1. The non-bonded interaction energy between PD-1 and PD-L1 ranges from − 1000 to − 2000 kJ mol^− 1 with a peak of 2700 frames at − 1600 kJ mol^− 1. The energy distribution between PD-1 and nivolumab ranges from − 500 to − 1200 kJ mol^− 1. The peak is at − 900 kJ mol^− 1 with 3100 occurrences. b The non-interaction energies between the BC-loop and two ligands is grouped into packages of 10 kJ mol^− 1. The energy between the BC-loop and PD-L1 peaks at-10 kJ mol^− 1. This peak occurs due to the minor distortions (between 0 and − 1 kJ mol^− 1). The non-bonded interaction energy between the BC-loop and nivolumab ranges from 0 to − 250 kJ mol^− 1