Characterization of peptide binding to the SARS-CoV-2 host factor neuropilin

Abstract

The ongoing coronavirus disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a global health concern. It is now well established that the spike (S) protein of SARS-CoV-2 interacts with its primary host receptor, the angiotensin converting enzyme 2 (ACE2). Additionally, the interaction of S with the neuropilin (NRP) receptor has been reported to facilitate viral entry. SARS-CoV-2 S protein binds to neuropilin-1 (NRP1) by virtue of a CendR motif which terminates with either an arginine or lysine. Furthermore, a number of different peptide sequences have been reported to bind to the same site in NRP1 including vascular endothelial growth factor A and other viral proteins. To gain a deeper understanding of additional factors besides the C-terminal arginine that may favour high NRP1 binding, several modelled peptides were investigated using triplicate 1 μs molecular dynamics simulations. A C-end histidine failed to exhibit strong NRP1 affinity. Some previously reported factors that increase binding affinity and secure NRP1 receptor activation was observed in the NRP1-peptide complexes studied and such complexes had higher molecular mechanics-generalized Born surface area based free energy of binding. Additionally, the results also highlight the relevance of an exposed arginine at its canonical location as capping it blocked arginine from engaging key residues at the NRP1 receptor site that are indispensable for functional binding; and that the presence of proline reinforces the C-terminal arginine. Given that stable NRP1 binding is crucial for viral uptake, stable interactions should be accounted for in the design of potential drugs and treatment routes to target or disrupt this interface, considering the S1-NRP1 interaction as well as its endogenous VEGF-A ligand that is associated with nociception.

Keywords: CendR motif; Molecular dynamics; Neuropilin; Spike protein; VEGF-A.

Figure 1

Structure of NRP1 in complex with S1 and alignment of the modelled peptides. (A) Structure of NRP1 (pink) in complex with S1 peptide fragment NSPRRAR (blue stick representation) (PDB ID:7JJC). Loop III region is shown in green. The flanking arginine residues of the S1 CendR motif RRAR is labelled in orange (B) Enlargement of A showing the NRP1-S1 binding interface and the residues that interact with both S1 and VEGF-A are labelled in orange. (C) An alignment of the mutated peptides used in this study. Amino acid numbering is based on the S1 peptide (NSPRRAR) bound to NRP1 in the structure 7JJC (chain G). The amino acids are colored based on the polarity of the sidechain; blue - positively charged; green - polar uncharged; orange – nonpolar.

Figure 2

Root mean square fluctuation (RMSF) of protein Cα atoms obtained from three independent runs of the different peptides bound to NRP1. (A) NRP1 protein in the NRP1–VEGF-A complex; (B) VEGF-A ligand in the NRP1–VEGF-A complex; (C) NRP1 protein in the NRP1–S1 complex; (D) NRP1 protein in the NRP1–R complex; (E) NRP1 protein in the NRP1–HRG complex; (F) NRP1 protein in the NRP1–RRRR complex; (G) NRP1 protein in the NRP1–RRAK complex; (H) NRP1 protein in the NRP1–RRAR complex; (I) NRP1 protein in the NRP1–RRAH complex; (J) NRP1 protein in the NRP1–TKPR complex; (K) NRP1 protein in the NRP1–TKPPR complex; (L) NRP1 protein in the NRP1–PPR complex; (M) NRP1 protein in the NRP1–PPRV complex; (N) NRP1 protein in the NRP1–PPR(V) complex; (O) NRP1 protein in the NRP1–EG0029 complex; (P) NRP1 protein in the NRP1– RRAA complex; (Q) NRP1 protein in the NRP1–RAAR complex; (R) NRP1 protein in the NRP1–ARAR complex.

Figure 3

The percentage of simulation time during which intermolecular polar contacts were retained between NRP1 and the peptides in three independent 1 μs runs of: (A) NRP1–RRAK; (B) NRP1–RRAH; (C) NRP1–RRRR; (D) NRP1–RRAR; (E) NRP1–VEGF-A; (F) NRP1–S1; (G) NRP1–R; (H) NRP1–HRG. When multiple types of polar interactions were observed between two residues, the superscript indicates the interaction type – h: hydrogen bond; s: salt bridge; p: π-cation.

Figure 4

The percentage of simulation time during which intermolecular polar contacts were retained between NRP1 and the peptides in three independent 1 μs runs of: (A) NRP1–PPR; (B) NRP1–PPRV; (C) NRP1– PPR(V); (D) NRP1–TKPR; (E) NRP1–TKPPR; (F) NRP1–RRAA; (G) NRP1–RAAR; (H) NRP1–ARAR; (I) NRP1–EG00229. When multiple types of polar interactions were observed between two residues, the superscript indicates the interaction type – h: hydrogen bond; s: salt bridge; p: π-cation; pp: π-π.

Figure 5

The percentage of simulation time during which intermolecular hydrophobic contacts were retained between NRP1 and the peptides in three independent 1 μs runs of: (A) NRP1–RRAR; (B) NRP1–RRAK; (C) NRP1–RRAH; (D) NRP1–VEGF-A; (E) NRP1–S1; (F) NRP1–PPR; (G) NRP1–PPRV; (H) NRP1– PPR(V); (I) NRP1–TKPPR; (J) NRP1–TKPR; (K) NRP1–RRAA; (L) NRP1–RAAR; (M) NRP1–ARAR.