Small RNA Viruses Research Articles

Evaluation of immune sensor responses to a viral small noncoding RNA.

Gammaherpesviruses are widespread pathogens causing persistent infections linked to the development of numerous types of lymphomas in humans. During latency, most of the viral protein-coding genes are suppressed, facilitating evasion of adaptive immune recognition of protein antigens. In contrast, many noncoding RNA (ncRNA) molecules are expressed in infected cells and can regulate key cellular pathways while simultaneously evading adaptive immune recognition. To counteract this, many cells express internal pattern recognition receptors that can intrinsically sense ongoing infections and initiate cellular defenses. Murine gammaherpesvirus 68 (MHV68) is a valuable model to study in vivo aspects of gammaherpesvirus pathogenesis. The MHV68 ncRNA TMER4 (tRNA-miRNA-encoding RNA 4) promotes lymph node egress of infected B cells: in the absence of TMER4, MHV68-infected B cells accumulate in the lymph node in a manner similar to B cells activated through specific antigen encounter. We hypothesized that TMER4 may alter intrinsic immune activation. In research described here, we aimed to explore the immunomodulatory functions of TMER4 by evaluating its impact on signaling through the critical immune sensors Toll-like receptor 4 (TLR4), TLR3, TLR7, and retinoic acid-inducible gene I (RIG-I). To accomplish this, we developed a system to test noncoding RNAs using commercially available reporter cell lines. We optimized the experimental procedure to ensure ncRNA expression and to quantify immune sensory molecule induction or inhibition by the expressed ncRNA. Expression of TMER4 RNAs from plasmid constructs did not alter TLR or RIG-I signaling. This study provides a clear experimental framework that can be applied to test other small ncRNAs for their impact on various innate immune sensor proteins.

Leader RNA facilitates snakehead vesiculovirus (SHVV) replication by interacting with CSDE1 and hnRNP A3

Leader RNAs are viral small non-coding RNAs that has been proved to play important roles in viral replication. Snakehead vesiculovirus (SHVV) is an aquatic virus that has caused huge economic loss in Chinese snakehead fish aquaculture industry. It has been proved that SHVV would generate leader RNA during the process of infection, and leader RNA could interact with viral nucleoprotein to promote viral replication. In this study, we identified that leader RNA could also interact with cellular protein Cold Shock Domain containing E1 (CSDE1) and heterogeneous nuclear ribonucleoproteins A3 (hnRNP A3). Further investigation reveals that overexpression of CSDE1 and hnRNP A3 facilitated SHVV replication. Downregulation of CSDE1 and hnRNP A3 by siRNA inhibited SHVV replication. This study provided a new sight into understand the mechanism of SHVV replication, and a potential anti-SHVV target for drug research.

Coxsackievirus B3 Activates Macrophages Independently of CAR-Mediated Viral Entry.

Enteroviruses are a genus of small RNA viruses that are responsible for approximately one billion global infections annually. These infections range in severity from the common cold and flu-like symptoms to more severe diseases, such as viral myocarditis, pancreatitis, and neurological disorders, that continue to pose a global health challenge with limited therapeutic strategies currently available. In the current study, we sought to understand the interaction between coxsackievirus B3 (CVB3), which is a model enterovirus, and macrophage cells, as there is limited understanding of how this virus interacts with macrophage innate immune cells. Our study demonstrated that CVB3 can robustly activate macrophages without apparent viral replication in these cells. We also showed that myeloid cells lacked the viral entry receptor coxsackievirus and adenovirus receptor (CAR). However, the expression of exogenous CAR in RAW264.7 macrophages was unable to overcome the viral replication deficit. Interestingly, the CAR expression was associated with altered inflammatory responses during prolonged infection. Additionally, we identified the autophagy protein LC3 as a novel stimulus for macrophage activation. These findings provide new insights into the mechanisms of CVB3-induced macrophage activation and its implications for viral pathogenesis.

Pathobiological characterization of a novel duck picornavirus in duck in China

A novel strain of duck picornavirus was isolated from duck tissue in Taian, Shandong Province, in 2017 in our laboratory. The virus was amplified in specific-pathogen-free (SPF) chicken embryos, purified and then analyzed by whole genome sequencing, which revealed a new duck-derived small RNA virus that was designated as Duck/FC22/China/2017 (FC22, GenBank accession no. MN102111) based on its genome structure and phylogenetic relationship. An in-depth study revealed that the virus grew well on the Leghorn male hepatoma (LMH) cell line. After propagation of the virus, SPF ducks were inoculated for pathogenicity tests, and their mental state, growth and development were observed after inoculation; the ducks were dissected to observe the organs and histopathological changes. A TaqMan fluorescence quantitative PCR method was utilized to detect the proliferation and shedding patterns of the virus within the ducks, while the SYBR Green I fluorescence quantitative PCR method was used to assess cytokine expression levels in the organs. The results showed that following inoculation with the FC22 strain, the mental status of the SPF ducks remained unchanged. Mild oedema was observed in some tissue organs during dissection; however, no pathological changes, such as congestion or degeneration, were noted. Histopathological analysis revealed cellular necrosis in organs, including the heart, liver, and bursa of Fabricius, as well as a reduced volume and deep staining of certain neurons in the cerebrum. Following infection, the virus titres in various organs and in cloacal swabs of the SPF ducks peaked on the first day before gradually decreasing daily. By the 10th d, the virus titres in all organs had decreased to less than 101 copies/μL. Additionally, notable alterations were observed in the expression levels of the cytokines IFNα, IL6, IL10, and TNFα. This indicates that the FC22 strain does not cause significant disease in ducks. This report presents the initial study on a recently discovered picornavirus, offering a thorough and methodical examination of its pathogenic characteristics and provides a reference for the clinical evaluation and scientific strategies for the prevention and treatment of this particular picornavirus.

Zika virus non-coding RNAs antagonize antiviral responses by PKR-mediated translational arrest.

Zika virus (ZIKV) is an emerging mosquito-borne flavivirus that causes severe outbreaks in human populations. ZIKV infection leads to the accumulation of small non-coding viral RNAs (known as sfRNAs) that are crucial for evasion of antiviral responses and for viral pathogenesis. However, the mechanistic understanding of how sfRNAs function remains incomplete. Here, we use recombinant ZIKVs and ribosome profiling of infected human cells to show that sfRNAs block translation of antiviral genes. Mechanistically, we demonstrate that specific RNA structures present in sfRNAs trigger PKR activation, which instead of limiting viral replication, enhances viral particle production. Although ZIKV infection induces mRNA expression of antiviral genes, translation efficiency of type I interferon and interferon stimulated genes were significantly downregulated by PKR activation. Our results reveal a novel viral adaptation mechanism mediated by sfRNAs, where ZIKV increases its fitness by repurposing the antiviral role of PKR into a proviral factor.

N6-methyladenosine modification of a parvovirus-encoded small noncoding RNA facilitates viral DNA replication through recruiting Y-family DNA polymerases

Human bocavirus 1 (HBoV1) is a human parvovirus that causes lower respiratory tract infections in young children. It contains a single-stranded (ss) DNA genome of ~5.5 kb that encodes a small noncoding RNA of 140 nucleotides known as bocavirus-encoded small RNA (BocaSR), in addition to viral proteins. Here, we determined the secondary structure of BocaSR in vivo by using DMS-MaPseq. Our findings reveal that BocaSR undergoes N6-methyladenosine (m6A) modification at multiple sites, which is critical for viral DNA replication in both dividing HEK293 cells and nondividing cells of the human airway epithelium. Mechanistically, we found that m6A-modified BocaSR serves as a mediator for recruiting Y-family DNA repair DNA polymerase (Pol) η and Pol κ likely through a direct interaction between BocaSR and the viral DNA replication origin at the right terminus of the viral genome. Thus, this report represents direct involvement of a viral small noncoding RNA in viral DNA replication through m6A modification.

Global genomics of Aedes aegypti unveils widespread and novel infectious viruses capable of triggering a small RNA response.

The mosquito Aedes aegypti is a prominent vector for arboviruses, but the breadth of mosquito viruses that infects this specie is not fully understood. In the broadest global survey to date of over 200 Ae. aegypti small RNA samples, we detected viral small interfering RNAs (siRNAs) and Piwi interacting RNAs (piRNAs) arising from mosquito viruses. We confirmed that most academic laboratory colonies of Ae. aegypti lack persisting viruses, yet two commercial strains were infected by a novel tombus-like virus. Ae. aegypti from North to South American locations were also teeming with multiple insect viruses, with Anphevirus and a bunyavirus displaying geographical boundaries from the viral small RNA patterns. Asian Ae. aegypti small RNA patterns indicate infections by similar mosquito viruses from the Americas and reveal the first wild example of dengue virus infection generating viral small RNAs. African Ae. aegypti also contained various viral small RNAs including novel viruses only found in these African substrains. Intriguingly, viral long RNA patterns can differ from small RNA patterns, indicative of viral transcripts evading the mosquitoes' RNA interference (RNAi) machinery. To determine whether the viruses we discovered via small RNA sequencing were replicating and transmissible, we infected C6/36 and Aag2 cells with Ae. aegypti homogenates. Through blind passaging, we generated cell lines stably infected by these mosquito viruses which then generated abundant viral siRNAs and piRNAs that resemble the native mosquito viral small RNA patterns. This mosquito small RNA genomics approach augments surveillance approaches for emerging infectious diseases.

Clinical problems and treatment of patients with chronic hepatitis C

Chronic viral hepatitis C is a chronic inflammatory disease lasting more than 6 months with predominant damage to liver tissue due to infection with the hepatitis C virus, which can lead to serious consequences: liver cirrhosis, liver cancer (hepatocellular carcinoma), and death. The etiological factor of this disease is a small hepatotropic RNA virus from the Flaviviridae family. Infection with the hepatitis C virus in a greater proportion of cases (55–85 %) leads to a chronic course of the disease, and over the next decades in about a quarter of patients, it leads to the development of liver cirrhosis, which, in turn, can serve as the basis for the formation of hepatocellular carcinoma.

Removal of Pseudomonas type IV pili by a small RNA virus.

The retractile type IV pilus (T4P) is important for virulence of the opportunistic human pathogen Pseudomonas aeruginosa. The single-stranded RNA (ssRNA) phage PP7 binds to T4P and is brought to the cell surface through pilus retraction. Using fluorescence microscopy, we discovered that PP7 detaches T4P, which impairs cell motility and restricts the pathogen's virulence. Using cryo-electron microscopy, mutagenesis, optical trapping, and Langevin dynamics simulation, we resolved the structure of PP7, T4P, and the PP7/T4P complex and showed that T4P detachment is driven by the affinity between the phage maturation protein and its bound pilin, plus the pilus retraction force and speed, and pilus bending. Pilus detachment may be widespread among other ssRNA phages and their retractile pilus systems and offers new prospects for antibacterial prophylaxis and therapeutics.

Viral and host small RNA transcriptome analysis of SARS-CoV-1 and SARS-CoV-2-infected human cells reveals novel viral short RNAs

RNA viruses have been shown to express various short RNAs, some of which have regulatory roles during replication, transcription, and translation of viral genomes. However, short viral RNAs generated from SARS-CoV-1 and SARS-CoV-2 genomic RNAs remained largely unexplored, possibly due limitations of the widely used library preparation methods for small RNA deep sequencing and corresponding data processing. By analyzing publicly available small RNA sequencing datasets, we observed that human Calu-3 cells infected by SARS-CoV-1 or SARS-CoV-2 accumulate multiple previously unreported short viral RNAs. In addition, we verified the presence of the five most abundant SARS-CoV-2 short viral RNAs in SARS-CoV-2-infected human lung adenocarcinoma cells by quantitative PCR. Interestingly, the copy number of the observed SARS-CoV-2 short viral RNAs dramatically exceeded the expression of previously reported viral microRNAs in the same cells. We hypothesize that the reported SARS-CoV-2 short viral RNAs could serve as biomarkers for early infection stages due to their high abundance. Furthermore, unlike SARS-CoV-1, the SARS-CoV-2 infection induced significant (Benjamini-Hochberg-corrected p-value <0.05) deregulation of Y-RNA, transfer RNA, vault RNA, as well as more than 300 endogenous short RNAs that aligned predominantly to human protein-coding and long noncoding RNA transcripts. In particular, more than 20-fold upregulation of reads derived from Y-RNA (and several transfer RNAs) have been documented in RNA-seq datasets from SARS-CoV-2 infected cells. Finally, a significant proportion of short RNAs derived from full-length viral genomes also aligned to various human genome (hg38) sequences, suggesting opportunities to investigate regulatory roles of short viral RNAs during infection. Further characterization of the small RNA landscape of both viral and host genomes is clearly warranted to improve our understanding of molecular events related to infection and to design more efficient strategies for therapeutic interventions as well as early diagnosis.

Elevated viral small RNA profiling in cassava cultivars suppress the occurrence of Cassava brown streak disease (CBSD)

Cassava brown streak disease (CBSD), caused by cassava brown streak virus (CBSV) and; Ugandan cassava brown streak virus (UCBSV) causes the most destructive cassava disease in Tanzania. Thus, breeders urgently need CBSD-resistant cultivars to combat the impact of this disease, safeguard cassava production, improve the yields and secure food supply for communities reliant on this staple crop. In this study, we used four cassava cultivars; Albert, KBH 2002/135, KBH 2006/026 and Kiroba to explore how viral small interfering RNA (vsiRNAs), an antiviral silencing mechanism, confers CBSD resistance. Cassava plants were inoculated by grafting method using the single infection of CBSV, UCBSV and mixed infection of these viruses (co-infection). Total RNA was extracted from leaves of each cultivar followed by deep sequencing. The result showed that high level of vsiRNAs was produced in inoculated plants, with the most prominent class being 21 and 22 nucleotides. Kiroba produced the highest level of vsiRNA in both CBSV and UCBSV, whereas KBH 2006/026 produced high level of vsiRNA only with UCBSV infections. In contrast to UCBSV, inoculation with CBSV stimulated severe symptoms but relatively low levels of vsiRNA. Co-infection treatment showed a more complex interaction between the host and virus, with variations in the severity and amount of vsiRNA produced. We conclude that resistance to CBSD varies depending on the type of cultivar and virus species, and the occurrence of CBSD is suppressed in plants with elevated vsiRNA. Therefore, a good understanding on the resistance status of parental materials for breeding is recommended to breeders as a basis for improving cassava production.

Prevalence of Astroviruses in Different Animal Species in Poland.

Astroviruses (AstVs) are small RNA viruses characterized by a high mutation rate, the ability to recombine, and interspecies transmission, which allows them to infect a multitude of hosts including humans, companion animals, and farmed animals as well as wildlife. AstVs are stable in the environment, and their transmission is usually through the fecal-oral route or via contaminated water and food. Although direct zoonotic transmission was not confirmed, interspecies transmission events have occurred or have been indicated to occur in the past between wild and domestic animals and humans. They cause large economic losses, mainly in the poultry sector, due to gastroenteritis and mortality. In young children, they are the second most common cause of diarrhea. This study involved 166 intestine samples and pools of spleen, lymph node, and kidney samples collected from 352 wild animals, 52 pigs, and 31 companion animals. Astroviruses were detected in the intestine samples and were separately detected in pools of tissue samples prepared for individual animals using a heminested RT-PCR protocol. Amplicons were subjected to Sanger sequencing, and a phylogenetic analysis of 320 nt RNA-dependent RNA polymerase (RdRp) fragments referring to known nt sequences of astroviruses was performed. Astroviral RNA was detected in the intestine samples and/or tissue pools of red foxes (nine positive intestines and six positive tissue pools), rats (two positive intestines and three positive tissue pools), a cat (one AstV detected in an intestine sample), pigs (eight positive tissue pools), and wild boars (two positive pools of spleens, kidneys, and lymph nodes). No astroviral RNA was detected in wild mustelids, dogs, or other small wild animals including rodents. A phylogenetic analysis revealed that the astroviruses detected during this study were mostly host-specific, such as porcine, canine, and rat astroviruses that were highly homologous to the sequences of reference strains. In one of two wild boars, an AstV distinct to porcine species was found with the highest nt identity to Avastroviruses, i.e., turkey astroviruses, which suggests potential cross-species transmission of the virus, as previously described. Here, we present the first detection of astroviruses in the population of wild animals, companion animals, and pigs in Poland, confirming that astroviruses are frequent pathogens circulating in animals in the field. Our study also suggests potential cross-species transmission of Avaastrovirus to wild boars; however, further molecular characterization is needed.

Long-term Survival in a Patient With Transformation of Waldenström's Macroglobulinemia into DLBCL.

Waldenström's macroglobulinemia (WM) is a rare slow-growing B-cell lymphoma that is characterized by lymphoplasmacytic bone marrow infiltration and the production of monoclonal immunoglobulin M (IgM) paraprotein. In 5-10% of patients, WM undergoes transformation into diffuse large B-cell lymphoma (DLBCL), which is more aggressive, with poor prognosis and a low survival rate. Α 69-year-old woman was diagnosed with WM in 2009. She received six cycles of chemoimmunotherapy and a remarkable remission was achieved. However, in 2013 the disease transformed into DLBCL. The patient received chemotherapy and after the completion of the first cycle of therapy, the disease was significantly minimized. At the end of the therapy, there was no evidence of disease, and the patient remains disease-free. The cytogenetic profile of the patient did not reveal expression of BCL2 apoptosis regulator, BCL6 transcription repressor, Epstein-Barr virus small RNA, syndecan 1 nor cyclin D1. According to a staging system based on the platelet count, lactate dehydrogenase and previous treatment for WM, the described patient was classified as being at intermediate risk with an expected 2-year survival probability of 47% after WM transformation into DLBCL. However, the patient unexpectedly exceeded these prognostic indications. The findings for this patient are of great interest compared with the existing literature which suggests that the survival and prognosis for patients with transformed DLBCL are not favorable.

Method for Quantitative HDV RNA Detection: I, Manual Workflow (Serum and Liver Tissue) and II, Fully Automated High Throughput Workflow for Diagnostic Use.

The hepatitis delta virus (HDV) is a small RNA virus (1700 base pairs), which uses the surface proteins of the hepatitis B virus (HBV) as an envelope. Accurate and reliable quantitative detection of HDV RNA is central for scientific and translational clinical research or diagnostic purposes. However, HDV poses challenges for nucleic acid amplification techniques: (1) the circular genome displays high intramolecular base pairing; (2) high content of cytosine and guanine; and (3) enormous genomic diversity among the eight known HDV genotypes (GTs). Here, we provide step-by-step instructions for (A) a manual workflow to perform a quantitative HDV reverse transcription (RT)-PCR from serum and liver tissue and (B) a quantitative HDV RT-PCR assay with whole process control to be used for serum or plasma samples run on a fully automated system. Both assays target the conserved ribozyme region and demonstrate inclusivity for all eight HDV GTs. The choice of assay depends on the experimental needs and equipment availability. While the former is ideal for scientific research laboratories, the latter provides a useful tool in the field of translational research or diagnostics.

SARS-Cov-2 small viral RNA suppresses gene expression via complementary binding to mRNA 3' UTR.

SARS-CoV-2 (SC2) has been intensely studied since its emergence. However, the mechanisms of host immune dysregulation triggered by SC2 remain poorly understood. That said, it is well established that many prominent viral families encode microRNAs (miRNAs) or related small viral RNAs (svRNAs) capable of regulating human genes involved in immune function. Importantly, recent reports have shown that SC2 encodes its own svRNAs. In this study, we have identified 12 svRNAs expressed during SC2 infection and show that one of these svRNAs can regulate target gene expression via complementary binding to mRNA 3' untranslated regions (3'UTRs) much like human microRNAs.

Bioinformatic Approaches for Comparative Analysis of Viruses.

The field of viral genomic studies has experienced an unprecedented increase in data volume. New strains of known viruses are constantly being added to the GenBank database and so are completely new species with little or no resemblance to our databases of sequences. In addition to this, metagenomic techniques have the potential to further increase the number and rate of sequenced genomes. Besides, it is important to consider that viruses have a set of unique features that often break down molecular biology dogmas, e.g., the flux of information from RNA to DNA in retroviruses and the use of RNA molecules as genomes. As a result, extracting meaningful information from viral genomes remains a challenge and standard methods for comparing the unknown and our databases of characterized sequences may need adaptations. Thus, several bioinformatic approaches and tools have been created to address the challenge of analyzing viral data. This chapter offers descriptions and protocols of some of the most important bioinformatic techniques for comparative analysis of viruses. The authors also provide comments and discussion on how viruses' unique features can affect standard analyses and how to overcome some of the major sources of problems. Protocols and topics emphasize online tools (which are more accessible to users) and give the real experience of what most bioinformaticians do in day-by-day work with command-line pipelines. The topics discussed include (1) clustering related genomes, (2) whole genome multiple sequence alignments for small RNA viruses, (3) protein alignment for marker genes and species affiliation, (4) variant calling and annotation, and (5) virome analyses and pathogen identification.

A meta-analysis for vaccine protection rate of duck hepatitis a virus in mainland China in 2009–2021

BackgroundDuck hepatitis A virus (DHAV) is a single-stranded, positive-strand small RNA virus that causes a very high mortality rate in ducklings. The DHAV-3 subtype incidence rate has recently increased in China, causing great economic losses to the waterfowl breeding industry. We analyzed the protection rate of DHAV vaccines used in mainland China from 2009 to 2021 and evaluated the effectiveness of vaccine prevention and control to reduce the economic losses caused by DHAV to the waterfowl breeding industry. We screened five electronic research databases and obtained 14 studies and patents on the protection efficiency of DHAV-1 and DHAV-3 vaccines.ResultsMeta-analysis demonstrated that immunized ducklings produced higher antibody levels and had a significantly higher survival rate than non-immunized ducklings [relative risk (RR) = 12, 95% confidence interval (CI) 6–26, P < 0.01]. The age of the ducks and vaccine valence did not affect protection efficiency. Data source analysis of the vaccine protection rate demonstrated that the vaccines conferred immune protection for ducklings in both small-scale experiments and large-scale clinical conditions. The analysis results revealed that although the vaccines conferred protection, the immune protective effect differed between small-scale experimental conditions and large-scale clinical conditions. This might have been due to non-standard vaccination and environmental factors.ConclusionsDomestic DHAV vaccines can protect ducklings effectively. The subjects immunized (breeding ducks or ducklings) and vaccine valence had no effect on the protective effect. Both small-scale experiments and large-scale clinical conditions conferred immune protection on ducklings, but vaccine immunization under small-scale experimental conditions had slightly better protective effects than large-scale clinical immunization.

The Roles of the 5' and 3' Untranslated Regions in Human Astrovirus Replication.

Astroviruses are small nonenveloped single-stranded RNA viruses with a positive sense genome. They are known to cause gastrointestinal disease in a broad spectrum of species. Although astroviruses are distributed worldwide, a gap in knowledge of their biology and disease pathogenesis persists. Many positive-sense single-stranded RNA viruses show conserved and functionally important structures in their 5' and 3' untranslated regions (UTRs). However, not much is known about the role of the 5' and 3' UTRs in the viral replication of HAstV-1. We analyzed the UTRs of HAstV-1 for secondary RNA structures and mutated them, resulting in partial or total UTR deletion. We used a reverse genetic system to study the production of infectious viral particles and to quantify protein expression in the 5' and 3' UTR mutants, and we established an HAstV-1 replicon system containing two reporter cassettes in open reading frames 1a and 2, respectively. Our data show that 3' UTR deletions almost completely abolished viral protein expression and that 5' UTR deletions led to a reduction in infectious virus particles in infection experiments. This indicates that the presence of the UTRs is essential for the life cycle of HAstV-1 and opens avenues for further research.

Plant virus movement proteins originated from jelly-roll capsid proteins.

Numerous, diverse plant viruses encode movement proteins (MPs) that aid the virus movement through plasmodesmata, the plant intercellular channels. MPs are essential for virus spread and propagation in distal tissues, and several unrelated MPs have been identified. The 30K superfamily of MPs (named after the molecular mass of tobacco mosaic virus (TMV) MP, the classical model of plant virology) is the largest and most diverse MP variety, represented in 16 virus families, but its evolutionary origin remained obscure. Here, we show that the core structural domain of the 30K MPs is homologous to the jelly-roll domain of the capsid proteins (CPs) of small RNA and DNA viruses, in particular, those infecting plants. The closest similarity was observed between the 30K MPs and the CPs of the viruses in the families Bromoviridae and Geminiviridae. We hypothesize that the MPs evolved via duplication or horizontal acquisition of the CP gene in a virus that infected an ancestor of vascular plants, followed by neofunctionalization of one of the paralogous CPs, potentially through the acquisition of unique N- and C-terminal regions. During the subsequent coevolution of viruses with diversifying vascular plants, the 30K MP genes underwent explosive horizontal spread among emergent RNA and DNA viruses, likely permitting viruses of insects and fungi that coinfected plants to expand their host ranges, molding the contemporary plant virome.

Generation of host-directed and virus-specific antivirals using targeted protein degradation promoted by small molecules and viral RNA mimics

Targeted protein degradation (TPD), as exemplified by proteolysis-targeting chimera (PROTAC), is an emerging drug discovery platform. PROTAC molecules, which typically contain a target protein ligand linked to an E3 ligase ligand, recruit a target protein to the E3 ligase to induce its ubiquitination and degradation. Here, we applied PROTAC approaches to develop broad-spectrum antivirals targeting key host factors for many viruses and virus-specific antivirals targeting unique viral proteins. For host-directed antivirals, we identified a small-molecule degrader, FM-74-103, that elicits selective degradation of human GSPT1, a translation termination factor. FM-74-103-mediated GSPT1 degradation inhibits both RNA and DNA viruses. Among virus-specific antivirals, we developed viral RNA oligonucleotide-based bifunctional molecules (Destroyers). As a proof of principle, RNA mimics of viral promoter sequences were used as heterobifunctional molecules to recruit and target influenza viral polymerase for degradation. This work highlights the broad utility of TPD to rationally design and develop next-generation antivirals.