An intranasal ASO therapeutic targeting SARS-CoV-2

The COVID-19 pandemic is exacting an increasing toll worldwide, with new SARS-CoV-2 variants emerging that exhibit higher infectivity rates and that may partially evade vaccine and antibody immunity. Rapid deployment of non-invasive therapeutic avenues capable of preventing infection by all SARS-CoV-2 variants could complement current vaccination efforts and help turn the tide on the COVID-19 pandemic. Here, we describe a novel therapeutic strategy targeting the SARS-CoV-2 RNA using locked nucleic acid antisense oligonucleotides (LNA ASOs). We identified an LNA ASO binding to the 5′ leader sequence of SARS-CoV-2 ORF1a/b that disrupts a highly conserved stem-loop structure with nanomolar efficacy in preventing viral replication in human cells. Daily intranasal administration of this LNA ASO in the K18-hACE2 humanized COVID-19 mouse model potently (98-99%) suppressed viral replication in the lungs of infected mice, revealing strong prophylactic and treatment effects. We found that the LNA ASO also represses viral infection in golden Syrian hamsters, and is highly efficacious in countering all SARS-CoV-2 "variants of concern" tested in vitro and in vivo, including B.1.427, B.1.1.7, and B.1.351 variants. Hence, inhaled LNA ASOs targeting SARS-CoV-2 represents a promising therapeutic approach to reduce transmission of variants partially resistant to vaccines and monoclonal antibodies, and could be deployed intranasally for prophylaxis or via lung delivery by nebulizer to decrease severity of COVID-19 in infected individuals. LNA ASOs are chemically stable and can be flexibly modified to target different viral RNA sequences, and they may have particular impact in areas where vaccine distribution is a challenge, and could be stockpiled for future coronavirus pandemics.

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Circumstances and mechanisms of inhibition of translation by secondary structure in eucaryotic mRNAs.

Molecular and Cellular Biology ◽

10.1128/mcb.9.11.5134 ◽

1989 ◽

Vol 9 (11) ◽

pp. 5134-5142 ◽

Cited By ~ 393

Author(s):

M Kozak

Keyword(s):

Secondary Structure ◽

Ribosomal Subunit ◽

Loop Structure ◽

Entry Site ◽

Range Interaction ◽

Stem Loop ◽

Stem Loop Structure ◽

Delta G

This paper describes in vitro experiments with two types of intramolecular duplex structures that inhibit translation in cis by preventing the formation of an initiation complex or by causing the complex to be abortive. One stem-loop structure (delta G = -30 kcal/mol) prevented mRNA from engaging 40S subunits when the hairpin occurred 12 nucleotides (nt) from the cap but had no deleterious effect when it was repositioned 52 nt from the cap. This result confirms prior in vivo evidence that the 40S subunit-factor complex, once bound to mRNA, has considerable ability to penetrate secondary structure. Consequently, translation is most sensitive to secondary structure at the entry site for ribosomes, i.e., the 5' end of the mRNA. The second stem-loop structure (hp7; delta G = -61 kcal/mol, located 72 nt from the cap) was too stable to be unwound by 40S ribosomes, hp7 did not prevent a 40S ribosomal subunit from binding but caused the 40S subunit to stall on the 5' side of the hairpin, exactly as the scanning model predicts. Control experiments revealed that 80S elongating ribosomes could disrupt duplex structures, such as hp7, that were too stable to be penetrated by the scanning 40S ribosome-factor complex. A third type of base-paired structure shown to inhibit translation in vivo involves a long-range interaction between the 5' and 3' noncoding sequences.

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Circumstances and mechanisms of inhibition of translation by secondary structure in eucaryotic mRNAs

Molecular and Cellular Biology ◽

10.1128/mcb.9.11.5134-5142.1989 ◽

1989 ◽

Vol 9 (11) ◽

pp. 5134-5142

Author(s):

M Kozak

Keyword(s):

Secondary Structure ◽

Ribosomal Subunit ◽

Loop Structure ◽

Entry Site ◽

Range Interaction ◽

Stem Loop ◽

Stem Loop Structure ◽

Delta G

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Two Xenopus Proteins That Bind the 3′ End of Histone mRNA: Implications for Translational Control of Histone Synthesis during Oogenesis

Molecular and Cellular Biology ◽

10.1128/mcb.19.1.835 ◽

1999 ◽

Vol 19 (1) ◽

pp. 835-845 ◽

Cited By ~ 52

Author(s):

Zeng-Feng Wang ◽

Thomas C. Ingledue ◽

Zbigniew Dominski ◽

Ricardo Sanchez ◽

William F. Marzluff

Keyword(s):

Translational Control ◽

Mrna Processing ◽

Loop Structure ◽

Histone Mrna ◽

Stem Loop ◽

Histone Mrnas ◽

Stem Loop Structure ◽

Histone Synthesis

ABSTRACT Translationally inactive histone mRNA is stored in frog oocytes, and translation is activated at oocyte maturation. The replication-dependent histone mRNAs are not polyadenylated and end in a conserved stem-loop structure. There are two proteins (SLBPs) which bind the 3′ end of histone mRNA in frog oocytes. SLBP1 participates in pre-mRNA processing in the nucleus. SLBP2 is oocyte specific, is present in the cytoplasm, and does not support pre-mRNA processing in vivo or in vitro. The stored histone mRNA is bound to SLBP2. As oocytes mature, SLBP2 is degraded and a larger fraction of the histone mRNA is bound to SLBP1. The mechanism of activation of translation of histone mRNAs may involve exchange of SLBPs associated with the 3′ end of histone mRNA.

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Opposing roles for Egalitarian and Staufen in transport, anchoring and localization of oskar mRNA in the Drosophila oocyte

PLoS Genetics ◽

10.1371/journal.pgen.1009500 ◽

2021 ◽

Vol 17 (4) ◽

pp. e1009500

Author(s):

Sabine Mohr ◽

Andrew Kenny ◽

Simon T. Y. Lam ◽

Miles B. Morgan ◽

Craig A. Smibert ◽

...

Keyword(s):

Binding Sites ◽

Inhibitory Effect ◽

Multiple Roles ◽

Rna Transport ◽

Nurse Cells ◽

Stem Loop ◽

Stem Loop Structure ◽

Dependent Inhibition

Localization of oskar mRNA includes two distinct phases: transport from nurse cells to the oocyte, a process typically accompanied by cortical anchoring in the oocyte, followed by posterior localization within the oocyte. Signals within the oskar 3’ UTR directing transport are individually weak, a feature previously hypothesized to facilitate exchange between the different localization machineries. We show that alteration of the SL2a stem-loop structure containing the oskar transport and anchoring signal (TAS) removes an inhibitory effect such that in vitro binding by the RNA transport factor, Egalitarian, is elevated as is in vivo transport from the nurse cells into the oocyte. Cortical anchoring within the oocyte is also enhanced, interfering with posterior localization. We also show that mutation of Staufen recognized structures (SRSs), predicted binding sites for Staufen, disrupts posterior localization of oskar mRNA just as in staufen mutants. Two SRSs in SL2a, one overlapping the Egalitarian binding site, are inferred to mediate Staufen-dependent inhibition of TAS anchoring activity, thereby promoting posterior localization. The other three SRSs in the oskar 3’ UTR are also required for posterior localization, including two located distant from any known transport signal. Staufen, thus, plays multiple roles in localization of oskar mRNA.

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Identification of Tau Stem Loop RNA Stabilizers

CrossRef Listing of Deleted DOIs ◽

10.1177/1087057107302676 ◽

2007 ◽

Vol 12 (6) ◽

pp. 789-799 ◽

Cited By ~ 26

Author(s):

Christine P. Donahue ◽

Jake Ni ◽

Eriks Rozners ◽

Marcie A. Glicksman ◽

Michael S. Wolfe

Keyword(s):

Small Molecules ◽

Binding Assay ◽

Loop Structure ◽

Stem Loop ◽

Binding Domains ◽

Stem Loop Structure ◽

Exon 10 ◽

Tau Expression

Alternative splicing of tau exon 10 produces tau isoforms with either 3 (3R) or 4 (4R) repeated microtubule-binding domains. Increased ratios of 4R to 3R tau expression, above the physiological 1:1, leads to neurofibrillary tangles and causes neurodegenerative disease. An RNA stem loop structure plays a significant role in determining the ratio, with decreasing stability correlating with an increase in 4R tau mRNA expression. Recent studies have shown that aminoglycosides are able to bind and stabilize the tau stem loop in vitro, suggesting that other druglike small molecules could be identified and that such molecules might lead to decreased exon 10 splicing in vivo. The authors have developed a fluorescent high-throughput fluorescent binding assay and screened a library of ∼110,000 compounds to identify candidate drugs that will bind the tau stem loop in vitro. In addition, they have developed a fluorescent-based RNA probe to assay the stabilizing effects of candiate drugs on the tau stem loop RNA. These assays should be applicable to the general problem of identifying small molecules that interact with mRNA secondary structures. ( Journal of Biomolecular Screening 2007:789-799)

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Designing P. aeruginosa synthetic phages with reduced genomes

Scientific Reports ◽

10.1038/s41598-021-81580-2 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Diana P. Pires ◽

Rodrigo Monteiro ◽

Dalila Mil-Homens ◽

Arsénio Fialho ◽

Timothy K. Lu ◽

...

Keyword(s):

Galleria Mellonella ◽

Antibacterial Properties ◽

Genetically Engineered ◽

In Vivo Studies ◽

Infection Model ◽

Promising Therapeutic Approach ◽

Genes Encoding ◽

First Time

AbstractIn the era where antibiotic resistance is considered one of the major worldwide concerns, bacteriophages have emerged as a promising therapeutic approach to deal with this problem. Genetically engineered bacteriophages can enable enhanced anti-bacterial functionalities, but require cloning additional genes into the phage genomes, which might be challenging due to the DNA encapsulation capacity of a phage. To tackle this issue, we designed and assembled for the first time synthetic phages with smaller genomes by knocking out up to 48% of the genes encoding hypothetical proteins from the genome of the newly isolated Pseudomonas aeruginosa phage vB_PaeP_PE3. The antibacterial efficacy of the wild-type and the synthetic phages was assessed in vitro as well as in vivo using a Galleria mellonella infection model. Overall, both in vitro and in vivo studies revealed that the knock-outs made in phage genome do not impair the antibacterial properties of the synthetic phages, indicating that this could be a good strategy to clear space from phage genomes in order to enable the introduction of other genes of interest that can potentiate the future treatment of P. aeruginosa infections.

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Specific Recognition of a Stem-Loop RNA Structure by the Alphavirus Capsid Protein

Viruses ◽

10.3390/v13081517 ◽

2021 ◽

Vol 13 (8) ◽

pp. 1517

Author(s):

Rebecca S. Brown ◽

Lisa Kim ◽

Margaret Kielian

Keyword(s):

Capsid Protein ◽

Rna Structure ◽

Semliki Forest Virus ◽

Virus Assembly ◽

Specific Binding ◽

Genomic Rna ◽

Stem Loop ◽

Stem Loop Structure ◽

Labeled Rna

Alphaviruses are small enveloped viruses with positive-sense RNA genomes. During infection, the alphavirus capsid protein (Cp) selectively packages and assembles with the viral genomic RNA to form the nucleocapsid core, a process critical to the production of infectious virus. Prior studies of the alphavirus Semliki Forest virus (SFV) showed that packaging and assembly are promoted by Cp binding to multiple high affinity sites on the genomic RNA. Here, we developed an in vitro Cp binding assay based on fluorescently labeled RNA oligos. We used this assay to explore the RNA sequence and structure requirements for Cp binding to site #1, the top binding site identified on the genomic RNA during all stages of virus assembly. Our results identify a stem-loop structure that promotes specific binding of the SFV Cp to site #1 RNA. This structure is also recognized by the Cps of the related alphaviruses chikungunya virus and Ross River virus.

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Synergistic In Vitro Antiretroviral Activity of a Humanized Monoclonal Anti-CD4 Antibody (TNX-355) and Enfuvirtide (T-20)

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00761-05 ◽

2006 ◽

Vol 50 (6) ◽

pp. 2231-2233 ◽

Cited By ~ 39

Author(s):

Xing-Quan Zhang ◽

Meredith Sorensen ◽

Michael Fung ◽

Robert T. Schooley

Keyword(s):

Viral Replication ◽

Viral Entry ◽

Antiretroviral Agents ◽

Entry Inhibitors ◽

High Level ◽

Antiretroviral Activity

ABSTRACT Recently, antiretroviral agents directed at several steps involved in viral entry have been shown to reduce viral replication in vitro and in vivo. We have demonstrated a high level of in vitro synergistic antiretroviral activity for two entry inhibitors that are directed at sequential steps in the entry process.

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MERS-CoV Accessory ORFs Play Key Role for Infection and Pathogenesis

mBio ◽

10.1128/mbio.00665-17 ◽

2017 ◽

Vol 8 (4) ◽

Cited By ~ 55

Author(s):

Vineet D. Menachery ◽

Hugh D. Mitchell ◽

Adam S. Cockrell ◽

Lisa E. Gralinski ◽

Boyd L. Yount ◽

...

Keyword(s):

Public Health ◽

Viral Replication ◽

Rapid Response ◽

Mutant Virus ◽

Global Public Health ◽

Vaccine Platform ◽

Zoonotic Pathogens ◽

Related Group

ABSTRACT While dispensable for viral replication, coronavirus (CoV) accessory open reading frame (ORF) proteins often play critical roles during infection and pathogenesis. Utilizing a previously generated mutant, we demonstrate that the absence of all four Middle East respiratory syndrome CoV (MERS-CoV) accessory ORFs (deletion of ORF3, -4a, -4b, and -5 [dORF3-5]) has major implications for viral replication and pathogenesis. Importantly, attenuation of the dORF3-5 mutant is primarily driven by dysregulated host responses, including disrupted cell processes, augmented interferon (IFN) pathway activation, and robust inflammation. In vitro replication attenuation also extends to in vivo models, allowing use of dORF3-5 as a live attenuated vaccine platform. Finally, examination of ORF5 implicates a partial role in modulation of NF-κB-mediated inflammation. Together, the results demonstrate the importance of MERS-CoV accessory ORFs for pathogenesis and highlight them as potential targets for surveillance and therapeutic treatments moving forward. IMPORTANCE The initial emergence and periodic outbreaks of MERS-CoV highlight a continuing threat posed by zoonotic pathogens to global public health. In these studies, mutant virus generation demonstrates the necessity of accessory ORFs in regard to MERS-CoV infection and pathogenesis. With this in mind, accessory ORF functions can be targeted for both therapeutic and vaccine treatments in response to MERS-CoV and related group 2C coronaviruses. In addition, disruption of accessory ORFs in parallel may offer a rapid response platform to attenuation of future emergent strains based on both SARS- and MERS-CoV accessory ORF mutants. IMPORTANCE The initial emergence and periodic outbreaks of MERS-CoV highlight a continuing threat posed by zoonotic pathogens to global public health. In these studies, mutant virus generation demonstrates the necessity of accessory ORFs in regard to MERS-CoV infection and pathogenesis. With this in mind, accessory ORF functions can be targeted for both therapeutic and vaccine treatments in response to MERS-CoV and related group 2C coronaviruses. In addition, disruption of accessory ORFs in parallel may offer a rapid response platform to attenuation of future emergent strains based on both SARS- and MERS-CoV accessory ORF mutants.

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