Viral Prefusion Targeting Using Entry Inhibitor Peptides: The Case of SARS-CoV-2 and Influenza A virus

Abstract

In this study, peptide entry inhibitors against the fusion processes of severe acute respiratory syndrome coronavirus-2 (SCV2) and influenza A virus (IAV) were designed and evaluated. Fusion inhibitor peptides targeting the conformational shift of the viral fusion protein were designed based on the relatively conserved sequence of HR2 from SCV2 spike protein and the conserved fusion peptide from hemagglutinin (HA) of IAV. Helical HR2 peptides bind more efficiently to HR1 trimer, while helical amphipathic anti-IAV peptides have higher cell penetration and endosomal uptake. The initial sequences were mutated by increasing the amphipathicity, using helix favoring residues, and residues likely to form salt- and disulfide-bridges. After docking against their targets, all anti-SCV2 designed peptides bonded with the HR1 3-helical bundle's hydrophobic crevice, while AntiSCV2P1, AntiSCV2P3, AntiSCV2P7, and AntiSCV2P8 expected to form coiled coils with at least one of the HR1 strands. Four of the designed anti-IAV peptides were cell-penetrating (AntiIAVP2, AntiIAVP3, AntiIAVP4, AntiIAVP7). All of them interacted with the fusion peptide of HA and some of the residues in the conserved hydrophobic pocket of HA2 in H1N1, H3N1, and H5N1 subtypes of IAV. AntiIAVP3 and AntiIAVP4 peptides had the best binding to HA2 conserved hydrophobic pocket, while, AntiIAVP2 and AntiIAVP6 showed the best binding to the fusion peptide region. According to analyses for in-vivo administration, AntiSCV2P1, AntiSCV2P7, AntiIAVP2, and AntiIAVP7 were the best candidates. AntiSCV2 and AntiIAV peptides were also conjugated using an in vivo cleavable linker sensitive to TMPRSS2 applicable as a single therapeutic in coinfections or uncertain diagnosis.