Inhibition of SARS-CoV-2 coronavirus proliferation by designer antisense-circRNAs

Abstract

Circular RNAs (circRNAs) are noncoding RNAs that exist in all eukaryotes investigated and are derived from back-splicing of certain pre-mRNA exons. Here, we report the application of artificial circRNAs designed to act as antisense-RNAs. We systematically tested a series of antisense-circRNAs targeted to the SARS-CoV-2 genome RNA, in particular its structurally conserved 5′-untranslated region. Functional assays with both reporter transfections as well as with SARS-CoV-2 infections revealed that specific segments of the SARS-CoV-2 5′-untranslated region can be efficiently accessed by specific antisense-circRNAs, resulting in up to 90% reduction of virus proliferation in cell culture, and with a durability of at least 48 h. Presenting the antisense sequence within a circRNA clearly proved more efficient than in the corresponding linear configuration and is superior to modified antisense oligonucleotides. The activity of the antisense-circRNA is surprisingly robust towards point mutations in the target sequence. This strategy opens up novel applications for designer circRNAs and promising therapeutic strategies in molecular medicine.

RETRACTED: Non-coding RNA in SARS-CoV-2: Progress toward therapeutic significance

“…Furthermore, unmodified antisense-circRNA was observed to be prevailing in activity compared to 2′-OMe- and 2′-MOE-modified antisense oligonucleotides and ultimately, it was remarkably resilient to point mutations in target sequences. As a result of their work, AS-circRNAs are established as suitable and novel molecular methods for targeting and functional regulation of distinct RNAs, thereby developing precise, flexible, and potent strategies for molecular virology and medicinal means of therapy [82] . Such encouraging establishments put RNA-based therapeutics forward into clinical trials regarding SARS-CoV-2.…”

Translational Control of COVID-19 and Its Therapeutic Implication

“…The most well-known examples are antisense oligonucleotides (ASOs), which contain modifications at their positions, such as 2-O-methyl (2-OME), 2-O-methoxy (2-MOE), locked nucleic acid (LNA), morpholino, or other nucleotide modifications, which may increase RNA base pairing, metabolic stability, and/or delivery ( 209 , 211 , 212 ). Circular RNAs (circRNAs) can also be engineered as antisense RNAs to disrupt SARS-CoV-2 genome expression and viral proliferation ( 213 ). These antisense-RNAs form stable hybrids with their target RNAs, which cause target RNAs cleavage/degradation or block mRNA processing or translation ( 213 – 215 ).…”

“…Circular RNAs (circRNAs) can also be engineered as antisense RNAs to disrupt SARS-CoV-2 genome expression and viral proliferation ( 213 ). These antisense-RNAs form stable hybrids with their target RNAs, which cause target RNAs cleavage/degradation or block mRNA processing or translation ( 213 – 215 ). Antisense DNA oligonucleotide forms a hybrid with the target RNA and induces cleavage of RNA by RNase H, an endonuclease that cleaves the RNA-DNA strands, limiting the synthesis of the encoded protein ( 212 ).…”

Past, Present and Future: The Relationship Between Circular RNA and Immunity

“…The best advantage is that the antisense sequence of circRNAs is better than the corresponding linear configuration and modified antisense oligonucleotides, and antisense circRNAs have strong activity against point mutations in the target sequence. This approach manifests the function of circRNAs as nucleic acid binders, starting novel applications for designing circRNAs and hopeful therapeutic strategies for COVID-19 ( 67 ). Fortunately, Qu et al.…”

“…identified a circRNA/lncRNA-miRNA–mRNA ceRNA network involving two circRNAs in SARS-CoV-2-infected cells, enhancing the current understanding of the mechanisms associated with coronavirus disease 2019 (COVID-19) ( 52 ). Specific segments of the SARS-CoV-2 5’-untranslated region can be expeditiously accessed by particular antisense circRNAs, resulting in bringing an approximately 90% cutback in virus proliferation in cell culture with a minimal duration of 2 days, which is attractive and promising ( 67 ). Briefly, relevant research focused on expression profile analyses, ceRNA construction and therapeutic target seeking.…”