Theoretical and Computational Chemistry

Using wide biological pores to cap and contain the COVID-19 spike protein



Geometric analysis shows that the spike (S) protein in the COVID-19 virus (SARS-Cov-2) can fully or partially enter into the channel of a wide biological pore like perforin (PFN) or streptolysin (SLO) when the latter is anchored in a bilayer lipid membrane. The PFN channel is a β barrel formed from multiple monomers, for example a ~14 nm diameter channel is formed from 22 monomers. Coincidentally the wide canopy of S (which has three identical chains) has an enclosing diameter of ~14 nm. While inside the channel peripheral residues in the canopy may bind with residues on the pore side of the barrel. If there are no adverse cross-reactions this would effectively prevent S from interacting with a target cell. Calculations with data obtained from PDB and other sources show that there are ~12 peripheral residue triples in S within a circle of diameter ~14 nm that can potentially bind with 22 exposed residues in each barrel monomer. The revised Miyazawa-Jernighan matrix is used to calculate the binding energy of canopy-PFN barrel residue pairs. The results show a large number of binding pairs over distances of up to 38 Å into the pore. This geometric view of capture and containment points to the possibility of using biological pores to neutralize SARS-Cov-2 in its many variant forms. Some necessary conditions that must be satisfied for such neutralization to occur are noted. A wide pore (such as PFN or SLO) can also be used in an electrolytic cell to detect the presence of SARS-Cov-2, which, by blocking the pore would cause a near total blockade of the base current (the ionic current in a fully open pore).

Version notes

Discussion expanded to include potential use of PFN or SLO in an electrolytic cell to detect presence of the virus in a sample based on pore current blockade. Abstract extended to reflect this addition.


Thumbnail image of chemrx-cov-spike-cap-np-2.pdf

Supplementary material

Thumbnail image of pore-cap-si-1.txt
6VXX data file
Residue coordinates and other information extracted from PDB for spike protein of SARS-Cov-2 (PDB id: 6VXX)
Thumbnail image of pore-cap-si-2.txt
Symmetrized Miyazawa-Jernighan matrix
Revised MJ matrix and its symmetrized version (upper triangle in former reflected across diagonal into lower triangle)