Amyloidogenic SARS-CoV-2 Spike Protein-Derived Peptides Form Oligomers and Selectively Damage Lipid Membranes

Several peptides derived from the SARS-CoV-2 spike protein (S-protein) are amyloidogenic, suggesting a potential role in COVID-19 disease-associated pathogenesis. Many disease-related amyloids form a variety of intermediate oligomeric aggregates and directly damage lipid membranes. Gain of toxic function is commonly observed for oligomeric and fibrillar aggregates of amyloid peptides. Therefore, the ability of four S-protein-derived peptides (s192, s258, s601, and s1166) to form oligomers and fibrils was investigated. Additionally, their ability to bind and damage lipid membranes was also determined. Using ThT assays, time points before and after fibril nucleation were chosen for each peptide to explore aggregate morphologies. At early time points, each peptide formed oligomers with unique morphological characteristics. Fibril morphologies of each peptide varied as well, with s601 and s1166 forming two distinct fibril morphologies that coexisted. When supported total brain lipid extract (TBLE) bilayers were exposed to S-protein-derived peptides and tracked via in situ AFM, only s192 progressively bound to and damaged the membrane. Oligomers of s1166 formed on TBLE bilayers but did not visibly disrupt the bilayer. Both the s258 and s601 minimally (if at all) interacted with the bilayers. No fibrils were observed on the bilayers from any of the peptides. The addition of Ca²⁺ to the assay reduced the ability of all peptides to bind to TBLE bilayers. As oligomer toxicity and membrane damage are common features of amyloid-based diseases, these results open the possibility that similar molecular mechanisms associated with the endoproteolysis of the SARS-CoV-2 S-protein may contribute to COVID-19.