The Prolyl-tRNA Synthetase Inhibitor Halofuginone Inhibits SARS-CoV-2 Infection

Sandoval, Daniel R.; Clausen, Thomas; Nora, Chelsea; Magida, Jason A.; Cribbs, Adam P.; Denardo, Andrea; Clark, Alex E.; Garretson, Aaron F.; Coker, Joanna; Narayanan, A.; Majowicz, Sydney A.; Philpott, Martin; Johansson, C.; Dunford, J E; Spliid, Charlotte B.; Golden, Gregory J.; Payne, N. Connor; Tye, Mark A; Nowell, Cameron J.; Griffis, Eric R.; Piermatteo, Ann; Grunddal, Kaare V.; Alle, Thibault; Hauser, Blake M.; Feldman, Jared; Caradonna, Timothy M.; Pu, Yuan; Yin, Xin; McVicar, Racheal N.; Tsimikas, Sotirios; Schmidt, Aaron; Ballatore, Carlo; Zengler, Karsten; Chanda, Sumit K.; Weiss, Ryan J.; Downes, Michael; Evans, Ronald M.; Croker, Ben A.; Leibel, Sandra L.; Jose, Joyce; Mazitschek, Ralph; Oppermann, U.; Carlin, Aaron F.; Gordts, Philip L.S.M.

doi:10.1101/2021.03.22.436522

Cited by 15 publications

(22 citation statements)

References 67 publications

(87 reference statements)

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“…We further explored the known function of CXCR6 associated with COVID-19 and other infectious diseases in case–control studies, phenome-wide association study (PheWAS) and GWAS. The association of the single-cell level phenotype (lower expression of CXCR6 and decreased proportion of CD8 + CXCR6 + T cells) and the severe COVID-19 has been observed in another work in circulating T cells with flow cytometry experiments (Payne et al 2021 ), suggesting the significant role of the chemokine receptor CXCR6 and its ligand CXCL16 in the immunopathogenesis of severe COVID-19. Another recent CRISPR screen study also suggested CXCR6 is one of the top-ranked genes, whose loss reduces SARS-CoV-2 infection in lung epithelial-like cells (Kasela et al 2021 ).…”

Section: Discussionmentioning

confidence: 55%

“…We identified and replicated three chemokine receptor genes, CXCR6 and CCR9 , with a protective effect in the lung and a risk effect in whole blood, respectively. CXCR6 is expressed in T lymphocytes and essential genes in CD8 + T RM cells, mediating the homing of T RM cells to the lung along with its ligand CXCL16 (Payne et al 2021 ; Wein et al 2019 ). CCR9 was reported to regulate chemotaxis in response to thymus-expressed chemokines in T cells (Lee et al 2012 ).…”

Section: Discussionmentioning

confidence: 99%

“…As illustrated in Fig. 5 , we hypothesized that host genetic variants or other unknown factors would lead to lower expression of CXCR6 , which might decrease the proportion of T RM cells residing in the lung through the CXCR6/CXCL16 axis (Payne et al 2021 ; Wein et al 2019 ), impairing the first-line defense. Moreover, the lower expression of CXCR6 might be related to the “unstable” residency of T RM cells in lung.…”

Section: Discussionmentioning

confidence: 99%

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Association of CXCR6 with COVID-19 severity: delineating the host genetic factors in transcriptomic regulation

et al. 2021

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The coronavirus disease 2019 (COVID-19) is an infectious disease that mainly affects the host respiratory system with ~ 80% asymptomatic or mild cases and ~ 5% severe cases. Recent genome-wide association studies (GWAS) have identified several genetic loci associated with the severe COVID-19 symptoms. Delineating the genetic variants and genes is important for better understanding its biological mechanisms. We implemented integrative approaches, including transcriptome-wide association studies (TWAS), colocalization analysis, and functional element prediction analysis, to interpret the genetic risks using two independent GWAS datasets in lung and immune cells. To understand the context-specific molecular alteration, we further performed deep learning-based single-cell transcriptomic analyses on a bronchoalveolar lavage fluid (BALF) dataset from moderate and severe COVID-19 patients. We discovered and replicated the genetically regulated expression of CXCR6 and CCR9 genes. These two genes have a protective effect on lung, and a risk effect on whole blood, respectively. The colocalization analysis of GWAS and cis -expression quantitative trait loci highlighted the regulatory effect on CXCR6 expression in lung and immune cells. In the lung-resident memory CD8 + T (T RM ) cells, we found a 2.24-fold decrease of cell proportion among CD8 + T cells and lower expression of CXCR6 in the severe patients than moderate patients. Pro-inflammatory transcriptional programs were highlighted in the T RM cellular trajectory from moderate to severe patients. CXCR6 from the 3p21.31 locus is associated with severe COVID-19. CXCR6 tends to have a lower expression in lung T RM cells of severe patients, which aligns with the protective effect of CXCR6 from TWAS analysis. Supplementary Information The online version contains supplementary material available at 10.1007/s00439-021-02305-z.

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Section: Discussionmentioning

confidence: 55%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Association of CXCR6 with COVID-19 severity: delineating the host genetic factors in transcriptomic regulation

et al. 2021

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“…In particular, halofuginone has been shown to exert pleotropic effects on the immune system (18) and has received orphan drug designation by the FDA in March 2020 for the treatment of scleroderma. More recently, halofuginone has been shown to be a potent inhibitor of SARS-CoV-2 infection in vitro, through two distinct putative mechanisms: down regulation of TMPRSS2 or through the effects of amino acid starvation on genomic biosynthesis and heparin sulfate decoration of proteoglycans on the cell surface (19,20).…”

Section: Resultsmentioning

confidence: 99%

SARS-CoV-2 spike protein 13-mer subdomain corresponds to the drug-binding domain of 3 glutamyl-propyl-tRNA synthetase 1 and is targetable by halofuginone

Benoit¹,

Shenoy²,

Meykler³

et al. 2021

Preprint

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Since its emergence, SARS-CoV-2 has been the subject of intense investigation. Early sequence analysis identified a unique 13 amino acid region (13-mer) nested within the receptor-binding domain (RBD) of the spike protein that directly interacts with the ACE2 receptor. Blasting with the 13-mer identified a highly conserved segment in propyl-tRNA synthetase enzymes. Comparison with the human analogue, glutamyl-propyl-tRNA synthetase 1, showed a high level of identity with its drug binding domain, which is targeted by halofuginone, a drug recently shown to block SARS-CoV-2 infection in vitro. In silico experiments predicted a high affinity interaction between halofuginone and the 13-mer. In vitro addition of halofuginone effectively inhibited binding of recombinant S1 monomer to ACE2. Accordingly, it appears that halofuginone inhibits viral infection by preventing correct interactions between spike protein and ACE2. These findings indicate that viral entry can potentially be drug-targeted and support the application of halofuginone in mitigation of COVID-19.

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“…While the complete translational value of our findings is unclear at this point in time, they support the possibility that antiviral drugs that promote amino acid starvation/synthesis by reducing fractions of rare codon tRNAs could be useful in blocking viral protein translation. One such example of a drug targeting protein translation is the prolyl-tRNA synthetase inhibitor halofuginone [ 54 ], which has been shown recently to be a potent inhibitor of SARS-CoV-2 infection and replication [ 55 ]. Further in-depth study of such drugs is clearly warranted.…”

Section: Discussionmentioning

confidence: 99%

The Functional Consequences of the Novel Ribosomal Pausing Site in SARS-CoV-2 Spike Glycoprotein RNA

Postnikova

Uppal

Huang

et al. 2021

IJMS

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The SARS-CoV-2 Spike glycoprotein (S protein) acquired a unique new 4 amino acid -PRRA- insertion sequence at amino acid residues (aa) 681–684 that forms a new furin cleavage site in S protein as well as several new glycosylation sites. We studied various statistical properties of the -PRRA- insertion at the RNA level (CCUCGGCGGGCA). The nucleotide composition and codon usage of this sequence are different from the rest of the SARS-CoV-2 genome. One of such features is two tandem CGG codons, although the CGG codon is the rarest codon in the SARS-CoV-2 genome. This suggests that the insertion sequence could cause ribosome pausing as the result of these rare codons. Due to population variants, the Nextstrain divergence measure of the CCU codon is extremely large. We cannot exclude that this divergence might affect host immune responses/effectiveness of SARS-CoV-2 vaccines, possibilities awaiting further investigation. Our experimental studies show that the expression level of original RNA sequence “wildtype” spike protein is much lower than for codon-optimized spike protein in all studied cell lines. Interestingly, the original spike sequence produces a higher titer of pseudoviral particles and a higher level of infection. Further mutagenesis experiments suggest that this dual-effect insert, comprised of a combination of overlapping translation pausing and furin sites, has allowed SARS-CoV-2 to infect its new host (human) more readily. This underlines the importance of ribosome pausing to allow efficient regulation of protein expression and also of cotranslational subdomain folding.

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The Prolyl-tRNA Synthetase Inhibitor Halofuginone Inhibits SARS-CoV-2 Infection

Cited by 15 publications

References 67 publications

Association of CXCR6 with COVID-19 severity: delineating the host genetic factors in transcriptomic regulation

Association of CXCR6 with COVID-19 severity: delineating the host genetic factors in transcriptomic regulation

SARS-CoV-2 spike protein 13-mer subdomain corresponds to the drug-binding domain of 3 glutamyl-propyl-tRNA synthetase 1 and is targetable by halofuginone

The Functional Consequences of the Novel Ribosomal Pausing Site in SARS-CoV-2 Spike Glycoprotein RNA

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