All SARS-CoV-2 variants have been inhibited by a easy peptide with nanomolar neutralization effectivity

In a latest research printed within the journal PNASresearchers from Finland and the USA reported a brand new heptad repeat 2 (HR2) peptide that inhibited extreme respiratory syndrome coronavirus 2 (SARS-CoV-2) with none chemical modifications.

Research: Nanomolar inhibition of SARS-CoV-2 an infection by an unmodified peptide focusing on the prehairpin intermediate of the spike protein. Picture Credit score: Kateryna Kon / Shutterstock

Background data

SARS-CoV-2 is constantly evolving with all variants of concern (VOCs) harboring mutations within the receptor binding area (RBD) of its spike (S) glycoprotein offering all 2019 coronavirus illness (COVID-19) vaccine and monoclonal antibody (mAb) therapies are ineffective.

There may be an pressing want for simpler antivirals towards SARS-CoV-2, particularly these focusing on buildings and processing which can be much less susceptible to mutation (eg, heptad repeats 1 and a couple of ( HR1-HR2) six-helix bundle of the SARS-CoV-2 S).

Beforehand, researchers have used a number of structural engineering strategies to make simpler HR2-based inhibitors primarily based on 36 amino acid segments of SARS-CoV-2 S 1168–1203 residues.

Concerning the research

Within the present research, researchers discovered that an unmodified SARS-CoV-2 HR2 peptide spanning S 1162–1203 residues referred to as longHR2_42 had a lot better SARS-CoV-2 inhibitory properties in comparison with its all earlier makes an attempt. They characterised the HR1-HR2 fold utilizing a molecular scaffolding methodology to substantiate its high-resolution cryo-electron microscopy (cryo-EM) construction of the longHR2_45 sure to HR1.

Subsequent, they designed an prolonged HR2 peptide with an extended N-terminal area spanning amino acid residues 1159–1179 utilizing Coot that achieved SARS-CoV-2 inhibition within the nanomolar (nM) vary. They outlined the construction in Rosetta utilizing the automated construction replace protocol. Likewise, they assessed HR1-HR2 complicated formation utilizing intrinsic fluorescence on clear native-polyacrylamide gel electrophoresis (CN-PAGE).

The researchers developed two assays to detect complicated formation between HR2 and HR1 variants and a cell-cell fusion assay to check the impact of the N-terminal extension of HR2 on inhibiting the membrane fusion perform of SARS-CoV-2 S.

The primary assay used cell floor de Escherichia coli to show HR2 peptides on an enhanced OmpX (eCPX)-protein scaffold. Subsequent, the researchers stimulated these cells with HR1-tagged inexperienced fluorescent protein (GFP) and GFP-positive cells expressing HR2 peptides that bind HR1, which they chose utilizing cell sorting on was activated by fluorescence (FAC). The second assay used messenger ribonucleic acid (mRNA) show to detect HR2-HR1 complicated formation.

Analysis findings

The novel N-terminal prolonged HR2 peptide developed within the present research confirmed ~100-fold stronger inhibition of all main SARS-CoV-2 variants, with a half-maximal inhibitory focus (IC).50) worth of ∼1 nM as assessed by a cell-based fusion assay. Notably, it had ∼10-fold decrease inhibitory exercise towards the Omicron variant. Three mutations within the HR1 area of Omicron – Q954H, N969K, and L981F – all nested within the area between HR1 and the N-terminal extension of HR2, explaining the weaker inhibitory exercise of longHR2_42.

Schematic of SARS-CoV-2 an infection and inhibition by HR2 peptides. (I) SARS-CoV-2 binds the host cell receptor ACE2 via interplay with the S1 area of protein S. (II) After cleavage by host cell proteases, the S1 area is launched and the S2 area of the S protein extends into the host cell membrane. (III) Stimulated by barely acidic pH, the S2 area folds again pulling the viral and host cell membranes into shut proximity, and (IV) folding of the HR1 and HR2 domains surrounds the viral membrane with the host cell membrane. (V) Within the presence of the inhibitor longHR2_42, the S protein enters the host cell receptor in the identical manner the place (VI) after cleavage the inhibitor longHR2_42 binds the HR1 area which (VII) prevents the folding of the HR1 and HR2 domains collectively and inhibits membrane fusion. On this mannequin, solely a subset of the potential binding websites for the inhibitor is required to inhibit fusion.

In opposition to Delta VOC, IC50 values ​​differed practically fivefold between VSV-SARS-CoV-2 infectivity evaluation and confirmed SARS-CoV-2 diagnoses.

As well as, the researchers famous that longHR2_42 didn’t present an identical improve within the obvious affinity for HR1 within the three binding assays described within the research. There are two doable explanations for a similar. First, these assays weren’t delicate sufficient to detect small adjustments in relationship. Nonetheless, it’s extra probably that different components affected the anti-SARS-CoV-2 efficacy of HR2-derived peptides.

Single virus imaging has revealed that 9 to 12 S proteins are required for SARS-CoV-2 fusion to retain mobile receptors; due to this fact, a single inhibitory protein may stop fusion. Additionally, protein S cleavage should require transmembrane serine protease 2 (TMPRSS2) or cathepsin. Because the researchers added dynamin inhibitor dynasore-OH to forestall cathepsin within the washing experiments, they established a prehairpin intermediate of SARS-CoV-2 S for peptide binding. Subsequently, with out TMPRSS2, the virus and peptide had a weak bond, thus limiting the lifetime of the vaccine to solely 15 to twenty minutes. Nonetheless, the noticed enhanced affinity of longHR2_42 was unbiased of host cell proteases required for S cleavage.


The HR2 helical area of SARS-CoV-2 S confirmed the potential to be a supply of potent peptide-based anti-SARS-CoV-2 therapeutics that will work towards its VOCs and longer viruses away. Moreover, the longHR2_42 peptide had a protracted inhibitory lifetime (greater than three hours) regardless of washout in virus infectivity assays, suggesting that it focused a pre-hairpin intermediate of SARS-CoV-2 S protein. In actual fact, the research knowledge offered additional assist for the pre-hairpin intermediate of the SARS-CoV-2 S glycoprotein.

In line with the authors, an extension of the longHR2_42 peptide sequence may improve its efficiency. As well as, its optimization sequence may additional enhance its exercise and supply a platform for growing different peptides particular to the SARS-CoV-2 variant.

Journal reference:

  • Nanomolar inhibition of SARS-CoV-2 an infection by an unmodified peptide focusing on the prehairpin intermediate of the spike protein. Kailu Yang, Chuchu Wang, Alex JB Kreutzberger, Ravi Ojha, Suvi Kuivanen, Sergio Couoh-Cardel, Serena Muratcioglu, Timothy J. Eisen, Ok. Ian White, Richard G. Held, Subu Subramanian, Kendra Marcus, Richard A. Pfuetzner, Luis Esquivies, Catherine A. Doyle, John Kuriyan, Olli Vapalahti, Giuseppe Balistreri, Tom Kirchhausen, and Axel T. Brunger, PNAS 2022, DOI:,

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