Neuropilin-1 assists SARS-CoV-2 infection by stimulating the separation of Spike protein S1 and S2

Abstract

The cell surface receptor Neuropilin-1 (Nrp1) was recently identified as a host factor for SARS-CoV-2 entry. Spike protein of SARS-CoV-2 is cleaved into two segments, the S1 (res. 1-685) and the S2 (res. 686-1273) domain by furin protease. Nrp1 predominantly binds to the C-terminal RRAR motif (res. 682-685) of the S1 domain. In this study, we firstly modeled the association of a Nrp1 protein (consisting of domains a2-b1-b2) with the Spike protein. Next, we studied the separation of S2 from the S1 domain, with and without Nrp1 bound, by utilizing molecular dynamics pulling simulations. During the separation, Nrp1 stabilizes the S1 C-terminal region (res. 640-685) and thereby assists the detachment of S2 N-terminal region (res. 686-700). Without Nrp1 bound, S1 tends to become stretched and thus the bound Nrp1 stimulates the earlier separation of S2 from the S1 domain. The liberated S2 domain is known to mediate the fusion of virus and host membranes, thus Nrp1 likely increases virus infectivity by facilitating the S1/S2 separation. We further analyzed the possible topological structure of the SARS-CoV-2 Spike protein when bound with Nrp1 and ACE2. Understanding of such a Nrp1-assisted viral infection opens the gate for the generation of protein-protein inhibitors, such as antibodies, which could attenuate the infection mechanism and protect certain cells in a future Nrp1:ACE2 targeted combination therapy.

Mechanisms of SARS-CoV-2 entry into cells

“…NRP1 was also shown to bind S1 through the multibasic furin-cleavage site and to promote S1 shedding and to expose the S2′ site to TMPRSS2 (ref. 124 ). Recently, the structure of ACE2 in complex with a neutral amino acid transporter, B0AT1, was analysed by cryo-EM in the presence and absence of the SARS-CoV-2 S protein 23 .…”

Human genetic basis of coronavirus disease 2019

“… 64 , 69 As the S protein is cleaved to the S1 and the S2 domain, the cell surface receptor neuropilin-1 (NRP1) may bind to the C-terminal functional furin-cleavage sequence of the S1 domain more strongly in some cases and help the S2 isolating from the S1 domain. 70 , 71 After S1 detachment, the S2 subunit undergoes a conformational change and mediates the fusion between the virus and the host membranes to mediate viral infection. 71 , 72 The virus enters the cytoplasm and starts the replication process to assemble new viral particles and amplify its viral load.…”

“… 70 , 71 After S1 detachment, the S2 subunit undergoes a conformational change and mediates the fusion between the virus and the host membranes to mediate viral infection. 71 , 72 The virus enters the cytoplasm and starts the replication process to assemble new viral particles and amplify its viral load. 69 , 73 During the viral entry and replication process, cyclophilin A is essential for viral replication and its interaction with CD147 may mediate SARS-CoV-2 entering the host cells.…”

ACE2 function in the pancreatic islet: Implications for relationship between SARS‐CoV‐2 and diabetes

“…Interestingly, one study showed that other newly discovered entry factors for SARS‐CoV‐2 such as NRP1 (Neuropilin 1) 71 , 72 , 73 , 74 and TFRC (Transferrin Receptor) 75 are rather highly co‐expressed with beta cell marker, INSULIN, in healthy pancreata. The study found that while there was no stark difference in ACE2 and TMPRSS2 protein expressions between alpha and beta cells in the islet, both being low, NRP1 and TFRC were selectively expressed in the beta cells with a relatively high expression.…”

“…22 Interestingly, TMPRSS2 expression was observed by the group in islets only in the control individuals; however, it was found in both endocrine and exocrine pancreas in the deceased patients. 22 Interestingly, one study showed that other newly discovered entry factors for SARS-CoV-2 such as NRP1 (Neuropilin 1) [71][72][73][74] and TFRC (Transferrin Receptor) 75 are rather highly co-expressed with beta cell marker, INSULIN, in healthy pancreata. The study found that while there was no stark difference in ACE2 and TMPRSS2 protein expressions between alpha and beta cells in the islet, both being F I G U R E 3 Graphical representation of how SARS-CoV-2 perturbs beta cell response upon direct invasion of pancreatic beta cells.…”