Safety and Biodistribution of Nanoligomers Targeting the SARS-CoV-2 Genome for the Treatment of COVID-19.

As the world braces to enter its fourth year of the coronavirus disease 2019 (COVID-19) pandemic, the need for accessible and effective antiviral therapeutics continues to be felt globally. The recent surge of Omicron variant cases has demonstrated that vaccination and prevention alone cannot quell the spread of highly transmissible variants. A safe and nontoxic therapeutic with an adaptable design to respond to the emergence of new variants is critical for transitioning to the treatment of COVID-19 as an endemic disease. Here, we present a novel compound, called SBCoV202, that specifically and tightly binds the translation initiation site of RNA-dependent RNA polymerase within the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome, inhibiting viral replication. SBCoV202 is a Nanoligomer, a molecule that includes peptide nucleic acid sequences capable of binding viral RNA with single-base-pair specificity to accurately target the viral genome. The compound has been shown to be safe and nontoxic in mice, with favorable biodistribution, and has shown efficacy against SARS-CoV-2 in vitro. Safety and biodistribution were assessed using three separate administration methods, namely, intranasal, intravenous, and intraperitoneal. Safety studies showed the Nanoligomer caused no outward distress, immunogenicity, or organ tissue damage, measured through observation of behavior and body weight, serum levels of cytokines, and histopathology of fixed tissue, respectively. SBCoV202 was evenly biodistributed throughout the body, with most tissues measuring Nanoligomer concentrations well above the compound KD of 3.37 nM. In addition to favorable availability to organs such as the lungs, lymph nodes, liver, and spleen, the compound circulated through the blood and was rapidly cleared through the renal and urinary systems. The favorable biodistribution and lack of immunogenicity and toxicity set Nanoligomers apart from other antisense therapies, while the adaptability of the nucleic acid sequence of Nanoligomers provides a defense against future emergence of drug resistance, making these molecules an attractive potential treatment for COVID-19.

Antisense Molecules Designed to Target SARS‐CoV‐2 are Nontoxic to the Host in a Murine Model

The COVID‐19 pandemic has demonstrated the dire need for new treatment strategies against infectious disease. COVID‐19 has caused over 766,000 deaths in the United States. While multiple vaccines have been developed, the occurrence of new variant strains and the low rates of vaccination in some regions threaten the efficacy of these vaccines in keeping the global population safe. Current treatments for patients with severe COVID‐19 mainly focus on controlling the immune response or providing organ support, but while most patients recover from the disease, lasting effects may continue to disrupt patient lives and global fatalities remain high. Here, we investigate the feasibility of using a novel antisense molecule as an antiviral against SARS‐CoV‐2. The antisense antiviral, called a nanoligomer, has been developed from Sachi Bioworks’ proprietary synthetic nucleic acid‐based drug discovery platform. The nanoligomers bind to specific DNA or mRNA sequences and offer high specificity and superior transport into cells. These molecules target the SARS‐CoV‐2 genome to prevent translation of the RNA‐dependent RNA polymerase ubiquitous in all RNA viruses, thus preventing viral replication. These antivirals were assessed for toxicity in mice using intranasal, intraperitoneal, and intravenous administration. Intranasal drug administration maximizes treatment concentration at the respiratory infection site, while intraperitoneal and intravenous administration gives further insight on biodistribution of the compound and responses in other organs. Data shows a favorable safety profile in our murine model. Body weight of mice was unaffected by administration of nanoligomers. Serum parameters and organ histology indicated no changes compared to control mice. Cytokine levels remained largely below the level of detection, suggesting that the nanoligomers did not cause any inflammation or immune response in the mice. Further, biodistribution studies showed high initial bioavailability to the lungs, followed by rapid renal clearance and urinary excretion. The nanoligomers therefore show traits of being a safe therapeutic with favorable bioavailability and desirable clearance post‐treatment. The antiviral presented is highly adaptable and the sequence may be adjusted to target new variants of respiratory viruses. The antisense sequence can additionally be designed to target a wide variety of DNA, mRNA, or miRNA, including host sequences linked to severe inflammatory responses to COVID‐19. A second nanoligomer we have designed and tested targets a human miRNA that has been shown to be upregulated in patients with severe symptoms in response to a SARS‐CoV‐2 infection. Binding this miRNA and preventing its action within the host may prevent damage to the host body caused by the immune response. The ability of these molecules to target either the virus itself or alleviate harmful host responses to infection makes nanoligomers a highly versatile treatment option for COVID‐19.

Nanoligomers Targeting Human miRNA for the Treatment of Severe COVID-19 Are Safe and Nontoxic in Mice.

The devastating effects of the coronavirus disease 2019 (COVID-19) pandemic have made clear a global necessity for antiviral strategies. Most fatalities associated with infection from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) result at least partially from uncontrolled host immune response. Here, we use an antisense compound targeting a previously identified microRNA (miRNA) linked to severe cases of COVID-19. The compound binds specifically to the miRNA in question, miR-2392, which is produced by human cells in several disease states. The safety and biodistribution of this compound were tested in a mouse model via intranasal, intraperitoneal, and intravenous administration. The compound did not cause any toxic responses in mice based on measured parameters, including body weight, serum biomarkers for inflammation, and organ histopathology. No immunogenicity from the compound was observed with any administration route. Intranasal administration resulted in excellent and rapid biodistribution to the lungs, the main site of infection for SARS-CoV-2. Pharmacokinetic and biodistribution studies reveal delivery to different organs, including lungs, liver, kidneys, and spleen. The compound was largely cleared through the kidneys and excreted via the urine, with no accumulation observed in first-pass organs. The compound is concluded to be a safe potential antiviral treatment for COVID-19.

Role of miR-2392 in driving SARS-CoV-2 infection.

MicroRNAs (miRNAs) are small non-coding RNAs involved in post-transcriptional gene regulation that have a major impact on many diseases and provide an exciting avenue toward antiviral therapeutics. From patient transcriptomic data, we determined that a circulating miRNA, miR-2392, is directly involved with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) machinery during host infection. Specifically, we show that miR-2392 is key in driving downstream suppression of mitochondrial gene expression, increasing inflammation, glycolysis, and hypoxia, as well as promoting many symptoms associated with coronavirus disease 2019 (COVID-19) infection. We demonstrate that miR-2392 is present in the blood and urine of patients positive for COVID-19 but is not present in patients negative for COVID-19. These findings indicate the potential for developing a minimally invasive COVID-19 detection method. Lastly, using in vitro human and in vivo hamster models, we design a miRNA-based antiviral therapeutic that targets miR-2392, significantly reduces SARS-CoV-2 viability in hamsters, and may potentially inhibit a COVID-19 disease state in humans.