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 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 and EG00229 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 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 CendR peptide binding affinity to 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.

Age-Related Differences in the Expression of Most Relevant Mediators of SARS-CoV-2 Infection in Human Respiratory and Gastrointestinal Tract

“…The results obtained in this study suggest that the lower severity of SARS-CoV-2 infection observed in children may be due to a different expression in the respiratory tract of NRP1, the pivotal co-receptor that enhance SARS-CoV-2 entry into the host cells (17,18). This data also support the potential role of NRP1 as therapeutic target against COVID-19, as suggested by others (33).…”

Neuropilin-1 in the pathogenesis of preeclampsia, HIV-1, and SARS-CoV-2 infection: A review

“…A novel study observed a significant reduction of cell infection following pre-incubation of SARS-CoV-2 pseudovirus with recombinant soluble extracellular b1b2 domain of NRP-1 ( Cantuti-Castelvetri et al, 2020 ). Several amino acid residues at the NRP-1 binding site (Y297, W301, N313, T316, P317, E319, D320, S346, E348, T349, K351, and Y353) have become a target of interest to block SARS-CoV-2 S1 interaction ( Klaewkla et al, 2021 ; Charoute et al, 2022 ). Two monoclonal antibodies and a known NRP-1 antagonist molecule, EG00229, exhibited a considerable decrease in SARS-CoV-2 infection in cell culture by disrupting the interaction between the spike protein and the b1 domain of NRP-1 through high specificity binding of the NRP-1 CendR motif ( Daly et al, 2020 ).…”

“…Two monoclonal antibodies and a known NRP-1 antagonist molecule, EG00229, exhibited a considerable decrease in SARS-CoV-2 infection in cell culture by disrupting the interaction between the spike protein and the b1 domain of NRP-1 through high specificity binding of the NRP-1 CendR motif ( Daly et al, 2020 ). Later comparisons highlighted that EG0137, R683G and A684M showed a greater affinity for the NRP-1 CendR binding region possibly due to interactions with more amino acid residues than EG00229 ( Klaewkla et al, 2021 ). Furthermore, the R683G and A684M peptides also displayed a higher NRP-1 binding efficiency than the SARS-CoV-2 S1 CendR heptapeptide ( Klaewkla et al, 2021 ).…”

“…Later comparisons highlighted that EG0137, R683G and A684M showed a greater affinity for the NRP-1 CendR binding region possibly due to interactions with more amino acid residues than EG00229 ( Klaewkla et al, 2021 ). Furthermore, the R683G and A684M peptides also displayed a higher NRP-1 binding efficiency than the SARS-CoV-2 S1 CendR heptapeptide ( Klaewkla et al, 2021 ).…”

Novel Small-Molecule Inhibitors of the SARS-CoV-2 Spike Protein Binding to Neuropilin 1

“…Interestingly, although the interaction with Asp320 was considered crucial for the binding, some studies suggested that a good affinity can also be achieved with antagonists lacking this interaction [40,42], expanding the possibilities for future structural modifications of small-molecule NRP1 antagonists. However, this interaction has still been recognised as critical for the SARS-CoV-2 binding [46], thus targeting it aims at successfully disrupting the SARS-CoV-2 NRP1 binding and is considered an attractive therapeutic approach to prevent viral entry. The well-known peptidomimetic NRP1 antagonist EG00229 (Figure 2A), which binds to the CendR-binding pocket and prevents the VEGF-A binding, was also evaluated for blocking the spike CendR binding in two different assays.…”