A Five-Helix-Based SARS-CoV-2 Fusion Inhibitor Targeting Heptad Repeat 2 Domain against SARS-CoV-2 and Its Variants of Concern

Abstract

The prolonged duration of the severe acute respiratory syndrome coronavirus−2 (SARS−CoV−2) pandemic has resulted in the continuous emergence of variants of concern (VOC, e.g., Omicron) and variants of interest (VOI, e.g., Lambda). These variants have challenged the protective efficacy of current COVID−19 vaccines, thus calling for the development of novel therapeutics against SARS−CoV−2 and its VOCs. Here, we constructed a novel fusion inhibitor−based recombinant protein, denoted as 5−Helix, consisting of three heptad repeat 1 (HR1) and two heptad repeat 2 (HR2) fragments. The 5−Helix interacted with the HR2 domain of the viral S2 subunit, the most conserved region in spike (S) protein, to block homologous six−helix bundle (6−HB) formation between viral HR1 and HR2 domains and, hence, viral S−mediated cell–cell fusion. The 5−Helix potently inhibited infection by pseudotyped SARS−CoV−2 and its VOCs, including Delta and Omicron variants. The 5−Helix also inhibited infection by authentic SARS−CoV−2 wild−type (nCoV−SH01) strain and its Delta variant. Collectively, our findings suggest that 5−Helix can be further developed as either a therapeutic or prophylactic to treat and prevent infection by SARS−CoV−2 and its variants.

Novel chimeric proteins mimicking SARS-CoV-2 spike epitopes with broad inhibitory activity

“…Our mimetic proteins specifically based on the SARS-CoV-2 S2 HR1 sequence constitute a novel approach to design this type of HR1-based fusion inhibitors targeting the highly conserved HR2 region. This approach is further supported by recent reports of a trimer of S2 HR1 polypeptides stabilized by conjugation to a foldon sequence [25] , and a S2 postfusion-based 5-helix construct [24] , both showing potent and broad inhibitory activities. Our strategy consisted however in engineering a single-chain polypeptide that can fold autonomously to mimic a highly stable HR1 surface, without any chemical modification or addition of external trimerization motifs.…”

“…HR1-based peptides are much less potent inhibitors [16] , [17] but stabilized mimics of a trimeric helical bundle based on the HIV-1 gp41 HR1 that target HR2 have shown potent inhibitory activity of HIV-1 fusion [20] , [21] , [22] and also inhibit human coronaviruses [23] . Moreover, a 5-helix construct based on the S2 6-HB structure but lacking one HR2 region has been reported very recently to inhibit several SARS-CoV-2 variants [24] . Also, trimers of S2 HR1 polypeptides stabilized by conjugation to a foldon sequence (HR1MFd) show broad coronavirus inhibitory activity [25] .…”

Potency of Fusion-Inhibitory Lipopeptides against SARS-CoV-2 Variants of Concern

“…The efficacy of SARS-CoV-2-inhibitory peptides at blocking viral transmission ( 7 , 19 , 20 ), taken together with our published data for other viruses ( 21 – 26 ), suggests that an effective antiviral effect can be achieved via administration of antiviral peptides. The potency of these lipopeptides for neutralization of SARS-CoV-2 VOCs is substantial and consistently observed across the VOCs.…”

An engineered 5-helix bundle derived from SARS-CoV-2 S2 pre-binds sarbecoviral spike at both serological- and endosomal-pH to inhibit virus entry

“…By targeting HR1, peptides derived from HR2 have been shown in several studies to be able to inhibit viral entry of SARS-CoV-2 and the related coronaviruses [ 26 , 27 , 34 ]. Reciprocally by targeting HR2, recombinant 5HB proteins have been successfully designed, for HIV, MERS-CoV and very recently for SARS-CoV-2[ 32 , 33 , 44 ], to block the virus infection. In the current study, we similarly focus on the fusion core of SARS-CoV-2 and have designed the 5HB proteins with clear anti-SARS-CoV-2 efficacy.…”