Novel Peptide Fusion Inhibitors for the Treatment of COVID-19

PROJECT SUMMARY COVID-19 is caused by inhalation of the latest coronavirus (CoV) SARS-CoV-2 into the lungs, and airway epithelia are particularly susceptible to uptake this virus. Extensive evidence indicates that angiotensin converting enzyme 2 (ACE2) binds to the S1 subunit of the SARS-CoV-2 Spike protein (S1), triggering selective proteolytic cleavage that liberates the S2 subunit. S2 undergoes extensive conformational changes to form a 6- helix bundle (6-HB) between Heptad Repeat (HR)-1 and HR-2 domains of S2, which ultimately results in the fusion of the viral particle with the cell membrane and subsequent viral entry. Based on the mechanism of viral entry, and supported by crystallography studies of the ACE2•S1 interface and the 6-HB complex of S2, enormous efforts are currently under way to develop peptide-based therapeutics to target both events: the interaction of SARS-CoV-2 Spike with ACE2 receptor, and the fusion of the viral particle to the cell membrane. We have discovered that exposure of well-differentiated, primary airway epithelial cultures to tobacco smoke for extended periods of time enhances ACE2 activity and increases binding of recombinant S1, which might explain the increased susceptibility of smokers to COVID-19. The Receptor Binding Domain (RBD) in S1 is part of a highly mutable region, as revealed by the appearance of multiple highly infectious SARS-CoV-2 variants in late 2020; thus, targeting this region might not be ideal for antiviral development. In contrast, the HR regions of the S2 subunit and the interaction mode of HR-1 and HR-2 domains within the 6-HB complex are highly conserved among various CoVs, which makes it an optimal target to develop broad-spectrum antivirals. EK1 is a peptide that. The goal of this application is to develop novel peptides that target the HR1 domain of the S2 subunit to inhibit membrane fusion and pseudovirus infection of SARS-CoV-2 as well as several other CoVs. These peptides should serve as broad-spectrum CoV antivirals for the treatment of COVID-19 and subsequent COVIDs. We propose to evaluate the proteolytic stability of several peptides in the hostile environment of the lung, as the main entry way of SARS-CoV-2, including stapled and N-capped peptides with enhanced helical constraint. We will measure the proteolytic stability of the peptides ex vivo using human lung secretions obtained from smokers and non-smokers. We will use primary airway epithelial cells to interrogate the ability of the peptides to inhibit fusion and SARS-CoV-2 pseudovirus infection to healthy and smoke-exposed airway cultures. The efficacy of these peptides will be ultimately evaluated in animal models. This study will address the feasibility of helical mimics to inhibit viral fusion and suppress viral entry into airway epithelia as a novel effective treatment against COVID-19.