Would It Be Possible to Stabilize Prefusion SARS-COV-2 Spikes with Ligands?

09 June 2021, Version 2
This content is a preprint and has not undergone peer review at the time of posting.


Fusion to host cells and infection caused by Severe Acute Respiratory Syndrome coronavirus (SARS)-CoV2 was inhibited in vitro by PP mutations stabilizing prefusion states of their spike (S) protein native conformation, as reported by several authors. However, the possible stabilization of S by binding-ligands, rather than by mutations, have not been explored, nor it is yet known if it would be possible. In this work, the so called “spring-loaded switch-folding” (SLSF) expanding S amino acid residues 960-1010 was computationally targeted because SLSF surrounded the previously described PP mutations. The SLSF trimeric prefusion conformation consisted in 3x3 α-helices that require a transition to 3 longer α-helices before viral/host membrane fusion, similarly to what occurs in other enveloped viruses. Results of a double computational screening among hundred of thousands of natural compounds for binding to the wild-type isolated SLSF conformer predicted more leads for its trimers than for monomers. Further ranked by the number of SLSF-conformers bound, some of the predicted top-leads may deserve experimental validation. Additional screening among thousands of drugs identified Tinosorb, an star-shaped molecule, as the lowest binding-score lead to SLSF in the low nM range. However, despite its lower binding-score, 3-fold molecular symmetry and fitting the inner part of the SLSF α-helices, we were unable to experimentally show any specific inhibition of S-mediated membrane fusion using an VSV-pseudotyped infectivity assay, nor any virtual binding to S-SLSF using docking to whole native S trimers. Further exploring the star-shaped features may provide new molecular alternatives to cross-bind the α-helices of S-SLSF to hypothetically inhibit coronavirus fusion.


S spike
computational screening
spring-loaded switch


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