Inhibition of SARS-CoV-2 (previously 2019-nCoV) infection by a highly potent pan-coronavirus fusion inhibitor targeting its spike protein that harbors a high capacity to mediate membrane fusion

Abstract

The recent outbreak of coronavirus disease caused by SARS-CoV-2 infection in Wuhan, China has posed a serious threat to global public health. To develop specific anti-coronavirus therapeutics and prophylactics, the molecular mechanism that underlies viral infection must first be defined. Therefore, we herein established a SARS-CoV-2 spike (S) protein-mediated cell-cell fusion assay and found that SARS-CoV-2 showed a superior plasma membrane fusion capacity compared to that of SARS-CoV. We solved the X-ray crystal structure of six-helical bundle (6-HB) core of the HR1 and HR2 domains in the SARS-CoV-2 S protein S2 subunit, revealing that several mutated amino acid residues in the HR1 domain may be associated with enhanced interactions with the HR2 domain. We previously developed a pan-coronavirus fusion inhibitor, EK1, which targeted the HR1 domain and could inhibit infection by divergent human coronaviruses tested, including SARS-CoV and MERS-CoV. Here we generated a series of lipopeptides derived from EK1 and found that EK1C4 was the most potent fusion inhibitor against SARS-CoV-2 S protein-mediated membrane fusion and pseudovirus infection with IC50s of 1.3 and 15.8 nM, about 241-and 149-fold more potent than the original EK1 peptide, respectively. EK1C4 was also highly effective against membrane fusion and infection of other human coronavirus pseudoviruses tested, including SARS-CoV and MERS-CoV, as well as SARSr-CoVs, and potently inhibited the replication of 5 live human coronaviruses examined, including SARS-CoV-2. Intranasal application of EK1C4 before or after challenge with HCoV-OC43 protected mice from infection, suggesting that EK1C4 could be used for prevention and treatment of infection by the currently circulating SARS-CoV-2 and other emerging SARSr-CoVs.

The anti-HIV Drug Nelfinavir Mesylate (Viracept) is a Potent Inhibitor of Cell Fusion Caused by the SARS-CoV-2 Spike (S) Glycoprotein Warranting further Evaluation as an Antiviral against COVID-19 infections

“…Transient expression of S-n and S-o glycoproteins produced drastic differences in cell fusion, while their overall protein expression was similar, as evidenced by immunohistochemistry signals obtained at 48 hpt. The enhanced fusogenicity of SARS CoV-2 versus SARS was recently noted in infection of Vero cells (40) further validating that our transient transfection results reflect Spikemediated virus-induced cell fusion differences between SARS and SARS CoV-2. Cell-surface expression of S-n and S-o was comparable suggesting that the observed differences in membrane fusion was due to inherent differences in the structure and function of S-n versus S-o glycoproteins.…”

Pharmacological Therapeutics Targeting RNA-Dependent RNA Polymerase, Proteinase and Spike Protein: From Mechanistic Studies to Clinical Trials for COVID-19

“…This provides a molecular mechanism in the binding of the antibody with S protein of SARS-CoV-2 [114]. In line with this result, recent study demonstrates a highly potent pan-coronavirus fusion inhibitor targeting its spike protein that harbors a high capacity to mediate membrane fusion, and inhibited SARS-CoV-2 infection [115]. The molecular mechanisms of coronavirus invasion into host cells will provide new insights into the development of therapeutic approaches for COVID-19 by targeting spike proteins and ACE2 [116][117][118].…”

Phylogenetic Analysis of the Novel Coronavirus Reveals Important Variants in Indian Strains

“…Spike protein has 89 been a hotspot in CoV2 genome since the beginning due to the presence of 90 receptor-binding domain. Contact point to the host includes the domains from S1 91 subunit of this S-protein [19]. The mutation observed 23403A>G (D614G) lies in tail 92 region of this S1 subunit and before the cleavage site of another subunit called S2 of 93 S-protein.…”

“…The 440 17 sequences are from different parts of the world including countries from Europe, USA, 18 Middle East, Asia and 28 sequences submitted from India with 11 sequenced in Iran. 19 The data was downloaded from GenBank, GISAID, and SRA. Data was collected for 20 this study last as of 9th April 2020, with 440 genome sequence of the novel and early 21 strains from the world along with 28 sequences from India.…”