Molecular basis of the new COVID-19 target neuropilin-1 in complex with SARS-CoV-2 S1 C-end rule peptide and small-molecule antagonists

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), responsible for causing the current coronavirus 2019 (COVID-19) pandemic, uses its spike (S1) protein for host cell attachment and entry. Apart from angiotensin-converting enzyme 2, neuropilin-1 (NRP1) has been recently found to serve as another host factor for SARS-CoV-2 infection; thus, blocking S1-NRP1 interaction can be a potential treatment for COVID-19. Herein, molecular recognition between SARS-CoV-2 S1 C-end rule (CendR) heptapeptide including small-molecule antagonists (EG00229 and EG01377) and the NRP1 was investigated using molecular dynamics simulations and binding free energy calculations based on MM-PBSA method. The binding affinity and the number of hot-spot residues of EG01377/NRP1 complex were higher than those of CendR/NRP1 and EG00229/NRP1 systems, in line with the reported experimental data as well as with the lower water accessibility at the ligand-binding site. The (i) T316, P317, and D320 and (ii) S346, T349, and Y353 residues of NRP1 were confirmed to respectively form H-bonds with the positively charged guanidinium group and the negatively charged carboxyl moiety of all studied ligands. Moreover, Rosetta protein design was employed to improve the binding affinity between CendR peptide and NRP1. The newly designed peptides, especially R683G and A684M, exhibited higher binding efficiency than the native CendR heptapeptide as well as the small-molecule EG00229 by forming more H-bonds and hydrophobic interactions with NPR1, suggesting that these designed peptides could be promising NRP1 inhibitors to combat SARS-CoV-2 infection.

Keywords: COVID-19; EG00229; EG01377; Neuropilin-1; SARS-CoV-2 S1 CendR.

Graphical abstract

Fig. 1

(A) Cartoon representation of SARS-CoV-2 infection. (B) Superimposed structures of NRP1 b1 domain in complex with CendR heptapeptide (PDB entry 7JJC) , EG00229 (PDB entry 3I97) , and EG01377 (PDB entry 6FMF) . (C) Chemical structure of all studied ligands.

Fig. 2

Time evolution of (top) all-atom RMSD and (bottom) #H-bonds of CendR heptapeptide (left), EG00229 (middle), and EG01377 (right) in complex with NRP1.

Fig. 3

SASA plots along the simulation time of the three studied systems.

Fig. 4

(A) $\mathrm{\Delta }{G}_{\text{bind}}^{\text{residue}}$ of CendR heptapeptide (left), EG00229 (middle), and EG01377 (right) in complex with NRP1 b1 coagulation factor domain. (B) Representative structures showing the ligand orientation in NRP1 b1 domain drawn from the last MD snapshot. The contributing residues of NRP1 involved in the binding of all studied ligands are colored according to their $\mathrm{\Delta }{G}_{\text{bind}}^{\text{residue}}$ values, where the highest to lowest free energies are shaded from white to red, respectively. (C) Electrostatic (ΔE_ele + ${\mathrm{\Delta }G}_{\text{solv}}^{\text{polar}}$, purple) and vdW (ΔE_vdW + ${\mathrm{\Delta }G}_{\text{solv}}^{\text{nonpolar}}$, magenta) energy contributions from each residue of NRP1 b1 domain to the binding of CendR (left), EG00229 (middle), and EG01377 (right).

Fig. 5

(A) Percentage of H-bond occupation of NRP1 contributing to the binding of (left) CendR heptapeptide, (middle) EG00229, and (right) EG01377. (B) Ligand orientation in the NRP1 b1 domain showing H-bond formations between protein and ligand(s). Orange dashed line indicates H-bond formation.

Fig. 6

(A) $\mathrm{\Delta }{G}_{\text{bind}}^{\text{residue}}$ of SARS-CoV-2 S1 CendR toward the binding of NRP1 b1 domain. (B) Representative structures showing the ligand orientation in NRP1 b1 domain drawn from the last MD snapshot. The contributing residues involved in the binding of CendR are colored according to its $\mathrm{\Delta }{G}_{\text{bind}}^{\text{residue}}$ values, where the highest to lowest free energies are shaded from white to red, respectively. (C) Percentage of H-bond occupation of NRP1 contributing to the binding of CendR peptide. (D) RMSD of each residue of CendR peptide along the simulation time.

Fig. 7

(A) ΔΔG_{bind(Rosetta)} (REU) of all designed peptides obtained from Rosetta. Note that the ΔΔG_bind was calculated using the following equation: ΔΔG_bind = ΔG_bind (mutant) – ΔG_bind (wild-type). (B) ΔG_bind (kcal/mol) of all designed peptides obtained from MM-PBSA method. (C) Representative structures of the two most promising peptides CendR_R683G and CendR_A684M showing the ligand orientation in NRP1 b1 domain drawn from the last MD snapshot. (D) $\mathrm{\Delta }{G}_{\text{bind}}^{\text{residue}}$ of CendR_WT, CendR_R683G, and CendR_A684M contributing to the binding of NRP1. (E) $\mathrm{\Delta }{G}_{\text{bind}}^{\text{residue}}$ of NRP1 contributing to the binding of CendR_WT, CendR_R683G, and CendR_A684M. (F) Percentage of H-bond occupation of NRP1 contributing to the binding of (left) CendR_WT, (middle) CendR_R683G, and (right) CendR_A684M. %H-bond occupation (%H-bond_oc) was classified into four levels: (i) strong H-bond (%H-bond_oc of > 75%), (ii) medium H-bond (75% ≥ %H-bond_oc > 50%), and (iii) weak H-bond (50% ≥ %H-bond_oc > 10%).