SARS-CoV-2 and bat RaTG13 spike glycoprotein structures inform on virus evolution and furin-cleavage effects

Wrobel, Antoni G.; Benton, D.J.; Xu, Pengqi; Roustan, Chloë; Martin, Stephen R.; Rosenthal, Peter B.; Skehel, J.J.; Gamblin, S.J.

doi:10.1038/s41594-020-0468-7

Cited by 551 publications

(754 citation statements)

References 33 publications

Supporting

Mentioning

676

Contrasting

Unclassified

Order By: Relevance

“…should be prioritized in light of efforts to develop ACE2 as a potential decoy therapeutic. Intelligent manipulation of ACE2 glycosylation may lead to more potent biologics capable of acting as better competitive inhibitors of S binding.The data presented here, and related similar recent findings(19,57,58), provide a framework to facilitate the production of immunogens, vaccines, antibodies, and inhibitors as well as providing additional information regarding mechanisms by which glycan microheterogeneity is achieved.However, considerable efforts still remain in order to fully understand the role of glycans in SARS-CoV-2 infection and pathogenicity. While HEK-expressed S and ACE2 provide a useful window for understanding human glycosylation of these proteins, glycoproteomic characterization following expression in cell lines of more direct relevance to disease and target tissue is sorely needed.…”

supporting

confidence: 80%

Virus-Receptor Interactions of Glycosylated SARS-CoV-2 Spike and Human ACE2 Receptor

Zhao

Praissman

Grant

et al. 2020

Preprint

View full text Add to dashboard Cite

SUMMARYThe current COVID-19 pandemic is caused by the SARS-CoV-2 betacoronavirus, which utilizes its highly glycosylated trimeric Spike protein to bind to the cell surface receptor ACE2 glycoprotein and facilitate host cell entry. We utilized glycomics-informed glycoproteomics to characterize site-specific microheterogeneity of glycosylation for a recombinant trimer spike mimetic immunogen and for a soluble version of human ACE2. We combined this information with bioinformatic analyses of natural variants and with existing 3D-structures of both glycoproteins to generate molecular dynamic simulations of each glycoprotein alone and interacting with one another. Our results highlight roles for glycans in sterically masking polypeptide epitopes and directly modulating Spike-ACE2 interactions. Furthermore, our results illustrate the impact of viral evolution and divergence on Spike glycosylation, as well as the influence of natural variants on ACE2 receptor glycosylation that, taken together, can facilitate immunogen design to achieve antibody neutralization and inform therapeutic strategies to inhibit viral infection.

show abstract

supporting

confidence: 80%

Virus-Receptor Interactions of Glycosylated SARS-CoV-2 Spike and Human ACE2 Receptor

Zhao

Praissman

Grant

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…For example, when titers are adjusted so that infections by SARS1-and SARS2-PV are identical in the presence of TMPRSS2 (Fig 1A), their efficiencies are markedly different in its absence. This difference can perhaps be explained by the relative instability of the wild-type SARS-CoV-2 S protein [16,39] in two ways. First, the furincleaved SARS-CoV S protein has been shown to prematurely shed [40], resulting in fewer S proteins per virion and pseudovirion.…”

Section: Discussionmentioning

confidence: 99%

Hydroxychloroquine-mediated inhibition of SARS-CoV-2 entry is attenuated by TMPRSS2

Mou

Zhang

et al. 2020

Preprint

View full text Add to dashboard Cite

Hydroxychloroquine, used to treat malaria and some autoimmune disorders, potently inhibits viral infection of SARS coronavirus (SARS-CoV-1) and SARS-CoV-2 in cell-culture studies. However, human clinical trials of hydroxychloroquine failed to establish its usefulness as treatment for COVID-19. This compound is known to interfere with endosomal acidification necessary to the proteolytic activity of cathepsins. Following receptor binding and endocytosis, cathepsin L can cleave the SARS-CoV-1 and SARS-CoV-2 spike (S) proteins, thereby activating membrane fusion for cell entry. The plasma membrane-associated protease TMPRSS2 can similarly cleave these S proteins and activate viral entry at the cell surface. Here we show that the SARS-CoV-2 entry process is more dependent than that of SARS-CoV-1 on TMPRSS2 expression. This difference can be reversed when the furin-cleavage site of the SARS-CoV-2 S protein is ablated. We also show that hydroxychloroquine efficiently blocks viral entry mediated by cathepsin L, but not by TMPRSS2, and that a combination of hydroxychloroquine and a clinically-tested TMPRSS2 inhibitor prevents SARS-CoV-2 infection more potently than either drug alone. These studies identify functional differences between SARS-CoV-1 and -2 entry processes, and provide a mechanistic explanation for the limited in vivo utility of hydroxychloroquine as a treatment for COVID-19.Author SummaryThe novel pathogenic coronavirus SARS-CoV-2 causes COVID-19 and remains a threat to global public health. Chloroquine and hydroxychloroquine have been shown to prevent viral infection in cell-culture systems, but human clinical trials did not observe a significant improvement in COVID-19 patients treated with these compounds. Here we show that hydroxychloroquine interferes with only one of two somewhat redundant pathways by which the SARS-CoV-2 spike (S) protein is activated to mediate infection. The first pathway is dependent on the endosomal protease cathepsin L and sensitive to hydroxychloroquine, whereas the second pathway is dependent on TMPRSS2, which is unaffected by this compound. We further show that SARS-CoV-2 is more reliant than SARS coronavirus (SARS-CoV-1) on the TMPRSS2 pathway, and that this difference is due to a furin cleavage site present in the SARS-CoV-2 S protein. Finally, we show that combinations of hydroxychloroquine and a clinically tested TMPRSS2 inhibitor work together to effectively inhibit SARS-CoV-2 entry. Thus TMPRSS2 expression on physiologically relevant SARS-CoV-2 target cells may bypass the antiviral activities of hydroxychloroquine, and explain its lack of in vivo efficacy.

show abstract

“…and its comparison to the Bat coronavirus RaTG13 isolate [20,21]. We found that at R-group classified sequences of N, B, A, and P in these two samples are identical up to level 4 of the amino acid ordering in the protein structures (Figures 4a, d, g).…”

Section: Resultsmentioning

confidence: 79%

“…This supports the findings of Wrobel et.al. [21]. (Figure 4g), but the higher-order comparison (Figures 4h, i) reveals key differences between these two viruses.…”

Section: Resultsmentioning

confidence: 98%

Ubiquitous Forbidden Order in R-group classified protein sequence of SARS-CoV-2 and other viruses

Pratibha

Shaju

Kamal

2020

Preprint

View full text Add to dashboard Cite

Each amino acid in a polypeptide chain has a distinctive R-group associated with it. We report here a novel method of species characterization based upon the order of these R-group classified amino acids in the linear sequence of the side chains associated with the codon triplets. In an otherwise pseudo-random sequence, we search for forbidden combinations of kth order. We applied this method to analyze the available protein sequences of various viruses including SARS-CoV-2. We found that these ubiquitous forbidden orders (UFO) are unique to each of the viruses we analyzed. This unique structure of the viruses may provide an insight into viruses chemical behavior and the folding patterns of the proteins. This finding may have a broad significance for the analysis of coding sequences of species in general

show abstract

SARS-CoV-2 and bat RaTG13 spike glycoprotein structures inform on virus evolution and furin-cleavage effects

Cited by 551 publications

References 33 publications

Virus-Receptor Interactions of Glycosylated SARS-CoV-2 Spike and Human ACE2 Receptor

Virus-Receptor Interactions of Glycosylated SARS-CoV-2 Spike and Human ACE2 Receptor

Hydroxychloroquine-mediated inhibition of SARS-CoV-2 entry is attenuated by TMPRSS2

Ubiquitous Forbidden Order in R-group classified protein sequence of SARS-CoV-2 and other viruses

Contact Info

Product

Resources

About