Nanomolar inhibition of SARS-CoV-2 infection by an unmodified peptide targeting the prehairpin intermediate of the spike protein

Abstract

Variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) challenge currently available coronavirus disease 2019 vaccines and monoclonal antibody therapies through epitope change on the receptor binding domain of the viral spike glycoprotein. Hence, there is a specific urgent need for alternative antivirals that target processes less likely to be affected by mutation, such as the membrane fusion step of viral entry into the host cell. One such antiviral class includes peptide inhibitors, which block formation of the so-called heptad repeat 1 and 2 (HR1HR2) six-helix bundle of the SARS-CoV-2 spike (S) protein and thus interfere with viral membrane fusion. We performed structural studies of the HR1HR2 bundle, revealing an extended, well-folded N-terminal region of HR2 that interacts with the HR1 triple helix. Based on this structure, we designed an extended HR2 peptide that achieves single-digit nanomolar inhibition of SARS-CoV-2 in cell-based and virus-based assays without the need for modifications such as lipidation or chemical stapling. The peptide also strongly inhibits all major SARS-CoV-2 variants to date. This extended peptide is ∼100-fold more potent than all previously published short, unmodified HR2 peptides, and it has a very long inhibition lifetime after washout in virus infection assays, suggesting that it targets a prehairpin intermediate of the SARS-CoV-2 S protein. Together, these results suggest that regions outside the HR2 helical region may offer new opportunities for potent peptide-derived therapeutics for SARS-CoV-2 and its variants, and even more distantly related viruses, and provide further support for the prehairpin intermediate of the S protein.

Cholesterol and ceramide facilitate SARS-CoV-2 Spike protein-mediated membrane fusion

“…So far, therapeutic strategies targeting the S2 fusion machinery mainly focused on the development of anti-fusogenic synthetic peptides mimicking the HR2 domain. Such peptides were shown to inhibit formation of the native HR1/HR2 six-helix coiled-coil hairpin complex, thus preventing viral fusion and infection by several human coronaviruses in situ, including MERS-CoV, SARS-CoV and SARS-CoV-2 [43][44][45] . Furthermore, intranasal injection of a synthetic lipopeptide derived from HR2 was found to protect ferrets against infection by SARS-CoV-2 46 .…”

Peptide-based inhibitors hold great promise as the broad-spectrum agents against coronavirus

“…Although previously reported HR1-derived peptide inhibitors exhibit poor inhibitory activities, foldon-mediated trimerization of the C-terminus conferred a HR1-derived peptide with higher inhibitory activity against SARS-CoV-2, SARS-CoV-2 variants of concern (VOCs), SARS-CoV, and MERS-CoV ( Bi et al, 2022 ). Moreover, an inspirational work identified that the extended N-terminus of HR2 also involves in interacting with HR1, and a synthetic peptide including this region achieved single-digit nanomolar inhibition of several SARS-CoV-2 variants ( Yang et al, 2022 ).…”

“…Compared to the conventional small molecule drugs, peptide synthesis can be quickly launched and modified ( Vagner et al, 2008 ; Gao et al, 2018 ). More importantly, the chemical composition makes peptides highly specific and effective to their targets, even at nanomolar or picomolar concentrations ( Cao et al, 2020 ; Schütz et al, 2020 ; Heydari et al, 2021 ; Shah et al, 2022 ; Yang et al, 2022 ).…”

Out With a Bang: Celebrating Global Chemical Biology

“…He then presented his inspiring latest research using large scale data visualization to achieve automated recognition of organelles from FIB-SEM data for both cultured cells and tissue using deep learning-aided image processing . The final part of his presentation was dedicated to his contribution to the research on SARS-CoV-2, where his laboratory characterized the infection route for the virus and helped discover a simple peptide exhibiting highly inhibitory properties against infections against SARS-CoV-2 variants to date …”

“…26 The final part of his presentation was dedicated to his contribution to the research on SARS-CoV-2, where his laboratory characterized the infection route for the virus 27 and helped discover a simple peptide exhibiting highly inhibitory properties against infections against SARS-CoV-2 variants to date. 28 After a restoring lunch break, the afternoon program was started by Prof. Paola Picotti (ETH Zurich, Switzerland), who shared her lab's latest results in revolutionizing proteomics to bring structural proteome snapshots into functional proteomics screens. Limited proteolysis-mass spectrometry (LiP-MS) not only allows the detection of small molecule binding to proteins through induced conformational changes but can also provide information on protein−protein binding or protein−metabolite interactions.…”