Dose-Dependent Influence of RBD-Derived Amyloidogenic Peptides on SARS-CoV-2 Infectivity: A Cautionary Tale for Antiviral Design.

The receptor-binding domain (RBD) of the SARS-CoV-2 Spike protein remains a central target for antiviral drug development. Recent in silico studies have revealed an expansion of amyloidogenic regions within the RBD of the Omicron variant, raising the possibility that amyloid-prone peptide fragments could modulate Spike function or host-virus interactions. In this study, we combined experimental assays with multiscale computational modeling to systematically characterise two short RBD-derived peptides: Pep-2 (YFPLQSYGFQ) from the ancestral Wuhan strain and Pep-3 (YFPLRSYSFR) from the Omicron BA.1 variant, the latter being predicted to have higher amyloidogenic potential. Cell-based assays demonstrated that neither peptide exhibited intrinsic cytotoxic or cytostatic effects on human lung fibroblasts or A549 lung adenocarcinoma cells at physiologically relevant concentrations, whereas significant cytotoxicity was observed in Vero E6 cells. In infection models with the B.1.1.1 (Wuhan) and BA.1 (Omicron) variants, the peptides unexpectedly enhanced virus-induced cytopathic effects at lower concentrations but inhibited viral infection at higher concentrations, indicating to a dose-dependent modulatory role for these short amyloidogenic RBD fragments. Fluorescence spectroscopy measurements did not detect the formation of stable thioflavin-T-positive amyloid fibrils. Computational analyses revealed that both peptides interact with the Spike RBD via multiple energetically favorable yet spatially heterogeneous modes, mostly outside the ACE2-binding site. Moreover, their predicted binding affinities for the ACE2 receptor were comparable, suggesting an additional route of interaction via the host receptor. Collectively, our findings demonstrate that these short amyloidogenic RBD-derived peptides exert a complex antiviral profile, with their interactions with both viral and host factors potentially shaping infection outcomes. This highlights the importance of spatially targeted and conformationally constrained peptide designs to effectively harness amyloidogenic features for antiviral therapy.