Site-specific cleavage of HCV genomic RNA and its cloned core and NS5B genes by DNAzyme

A promising nucleic acid therapy drug: DNAzymes and its delivery system

Based on the development of nucleic acid therapeutic drugs, DNAzymes obtained through in vitro selection technology in 1994 are gradually being sought. DNAzymes are single-stranded DNA molecules with catalytic function, which specifically cleave RNA under the action of metal ions. Various in vivo and in vitro models have recently demonstrated that DNAzymes can target related genes in cancer, cardiovascular disease, bacterial and viral infection, and central nervous system disease. Compared with other nucleic acid therapy drugs, DNAzymes have gained more attention due to their excellent cutting efficiency, high stability, and low cost. Here, We first briefly reviewed the development and characteristics of DNAzymes, then discussed disease-targeting inhibition model of DNAzymes, hoping to provide new insights and ways for disease treatment. Finally, DNAzymes were still subject to some restrictions in practical applications, including low cell uptake efficiency, nuclease degradation and interference from other biological matrices. We discussed the latest delivery strategy of DNAzymes, among which lipid nanoparticles have recently received widespread attention due to the successful delivery of the COVID-19 mRNA vaccine, which provides the possibility for the subsequent clinical application of DNAzymes. In addition, the future development of DNAzymes was prospected.

Specific DNAzymes cleave the 300-618 nt of 5'UTR to inhibit DHAV-1 translation and replication

DNAzymes effectively inhibit the expression of viral genes. Duck hepatitis A virus type-1 (DHAV-1) genomic RNA carries an internal ribosome entry site (IRES). The IRES initiates the translation of DHAV-1 via a mechanism that differs from that of cap-dependent translation. Therefore, it is an attractive target for the treatment of DHAV-1. In this study, we designed 6 DNAzymes (Dzs) specifically targeting 300-618 nt sequence in the DHAV-1 5'untranslated region (UTR; a predicted IRES-like element). In the presence of divalent metal ions, three designed DNAzymes (DZ369, DZ454, and DZ514) efficiently cleaved the 300-618 nt sequence of the DHAV-1 5'UTR RNA. The activity of the Dzs was particularly dependent on Mg²⁺ ions. Subsequently, the translation inhibitory activity of these Dzs was determined by western blotting experiments. The Dzs effectively inhibited the translation mediated by the 300-618 nt of DHAV-1 5'UTR in duck embryo fibroblasts (DEFs). Importantly, DZ454 showed the strongest inhibitory effect, and its inhibition was time and dose dependent. However, none of the Dzs showed significant inhibition of cap-dependent translation. These results suggest that these Dzs show specificity for target RNA. Moreover, DZ454 inhibited the replication of DHAV-1. In conclusion, the designed DNAzymes can be used as inhibitors of DHAV-1 RNA translation and replication, providing new insights useful for the development of anti-DHAV-1 drugs.

Reprogramming translation for gene therapy

Translational control plays a fundamental role in the regulation of gene expression in eukaryotes. Modulating translational efficiency allows the cell to fine-tune the expression of genes, spatially control protein localization, and trigger fast responses to environmental stresses. Translational regulation involves mechanisms acting on multiple steps of the protein synthesis pathway: initiation, elongation, and termination. Many cis-acting elements present in the 5' UTR of transcripts can influence translation at the initiation step. Among them, the Kozak sequence impacts translational efficiency by regulating the recognition of the start codon; upstream open reading frames (uORFs) are associated with inhibition of translation of the downstream protein; internal ribosomal entry sites (IRESs) can promote cap-independent translation. CRISPR-Cas technology is a revolutionary gene-editing tool that has also been applied to the regulation of gene expression. In this chapter, we focus on the genome editing approaches developed to modulate the translational efficiency with the aim to find novel therapeutic approaches, in particular acting on the cis-elements, that regulate the initiation of protein synthesis.

Advances in Targeting the Innate and Adaptive Immune Systems to Cure Chronic Hepatitis B Virus Infection

“Functional cure” is being pursued as the ultimate endpoint of antiviral treatment in chronic hepatitis B (CHB), which is characterized by loss of HBsAg whether or not anti-HBs antibodies are present. “Functional cure” can be achieved in <10% of CHB patients with currently available therapeutic agents. The dysfunction of specific immune responses to hepatitis B virus (HBV) is considered the major cause of persistent HBV infection. Thus, modulating the host immune system to strengthen specific cellular immune reactions might help eliminate HBV. Strategies are needed to restore/enhance innate immunity and induce HBV-specific adaptive immune responses in a coordinated way. Immune and resident cells express pattern recognition receptors like TLRs and RIG I/MDA5, which play important roles in the induction of innate immunity through sensing of pathogen-associated molecular patterns (PAMPs) and bridging to adaptive immunity for pathogen-specific immune control. TLR/RIG I agonists activate innate immune responses and suppress HBV replication in vitro and in vivo, and are being investigated in clinical trials. On the other hand, HBV-specific immune responses could be induced by therapeutic vaccines, including protein (HBsAg/preS and HBcAg), DNA, and viral vector-based vaccines. More than 50 clinical trials have been performed to assess therapeutic vaccines in CHB treatment, some of which display potential effects. Most recently, using genetic editing technology to generate CAR-T or TCR-T, HBV-specific T cells have been produced to efficiently clear HBV. This review summarizes the progress in basic and clinical research investigating immunomodulatory strategies for curing chronic HBV infection, and critically discusses the rather disappointing results of current clinical trials and future strategies.

Redox-responsive chitosan oligosaccharide-SS-Octadecylamine polymeric carrier for efficient anti-Hepatitis B Virus gene therapy

DrzBC and DrzBS (10-23 DNAzyme) could block the expression of HBV e- and s- gene respectively. But the application of 10-23 DNAzyme was limited owing to the lack of appropriate delivery vehicles. Chitosan oligosaccharide-SS-Octadecylamine (CSSO), a redox-responsive nano-sized polymeric carrier, could self-aggregate and bind with DNA by electrostatic interaction at proper mass ratio. Compared with the traditional commercial carrier Lipo2000, CSSO exhibited lower cytotoxicity, efficient cellular uptake by targeting cells, and rapidly DNA released in cytoplasm after escaping from endosomes. Including the same DNA concentration, Lipo2000/(DrzBC or DrzBS) showed maximum inhibitory rate on HBeAg (47.29 ± 1.86%) and HBsAg (33.58 ± 0.72%) secretion after 48 h incubation, and then both decreased. In contrast, HBeAg secretion inhibition by CSSO/DrzBC and HBsAg secretion inhibition by CSSO/DrzBS were up to 73.86 ± 1.77% and 67.80 ± 2.51% at 48 h, and further increased to 83.83 ± 2.34% and 76.79 ± 2.18% at 72 h, respectively. CSSO is a promising redox-responsive polymeric carrier for efficient anti-Hepatitis B Virus gene therapy.

Hepatitis B virus S gene therapy with 10-23 DNAzyme delivered by chitosan-g-stearic acid micelles

DrzBS, which targets HBV S gene expression, has important research significance and potential application value. CSO-SA is a safe and efficient non-viral gene carrier and CSO-SA/DrzBS micelles are a promising application for anti-HBV gene therapy.

Enteroviruses: Classification, Diseases They Cause, and Approaches to Development of Antiviral Drugs

The genus Enterovirus combines a portion of small (+)ssRNA-containing viruses and is divided into 10 species of true enteroviruses and three species of rhinoviruses. These viruses are causative agents of the widest spectrum of severe and deadly epidemic diseases of higher vertebrates, including humans. Their ubiquitous distribution and high pathogenici- ty motivate active search to counteract enterovirus infections. There are no sufficiently effective drugs targeted against enteroviral diseases, thus treatment is reduced to supportive and symptomatic measures. This makes it extremely urgent to develop drugs that directly affect enteroviruses and hinder their development and spread in infected organisms. In this review, we cover the classification of enteroviruses, mention the most common enterovirus infections and their clinical man- ifestations, and consider the current state of development of anti-enteroviral drugs. One of the most promising targets for such antiviral drugs is the viral Internal Ribosome Entry Site (IRES). The classification of these elements of the viral mRNA translation system is also examined.

Exploring Internal Ribosome Entry Sites as Therapeutic Targets

Initiation of eukaryotic mRNA translation may proceed via several different routes, each requiring a different subset of factors and relying on different and specific interactions between the mRNA and the ribosome. Two modes predominate: (i) so-called cap-dependent initiation, which requires all canonical initiation factors and is responsible for about 95–97% of all initiation events in eukaryotic cells; and (ii) cap-independent internal initiation, which requires a reduced subset of initiation factors and accounts for up to 5% of the remaining initiation events. Internal initiation relies on the presence of so-called internal ribosome entry site (IRES) elements in the 5′ UTRs of some viral and cellular mRNAs. These elements (often possessing complex secondary and tertiary structures) promote efficient interaction of the mRNA with the 40S ribosome and allow for internal ribosome entry. Internal initiation of translation of specific mRNAs may contribute to development of severe disease and pathological states, such as hepatitis C and cancer. Therefore, this cellular mechanism represents an attractive target for pharmacological modulation. The purpose of this review is to provide insight into current strategies used to target viral and cellular IRESs and discuss the physiological consequences (and potential therapeutic implications) of abrogation/modulation of IRES-mediated translation.

DNA enzymes as potential therapeutics: towards clinical application of 10-23 DNAzymes

INTRODUCTION

Ongoing studies on the inhibition of gene expression at the mRNA level have identified several types of specific inhibitors such as antisense oligonucleotides, small interfering RNA, ribozymes and DNAzymes (Dz). After its discovery in 1997, the 10-23 Dz (which can cleave RNA efficiently and site-specifically, has flexible design, is independent from cell mechanisms, does not require expensive chemical modifications for effective use in vivo) has been employed to downregulate a range of therapeutically important genes. Recently, 10-23 Dzs have taken their first steps into clinical trials.

AREAS COVERED

This review focuses predominantly on Dz applications as potential antiviral, antibacterial, anti-cancer and anti-inflammatory agents as well as for the treatment of cardiovascular disease and diseases of CNS, summarizing results of their clinical trials up to the present day.

EXPERT OPINION

In comparison with antisense oligonucleotides and small interfering RNAs, Dzs do not usually show off-target effects due to their high specificity and lack of immunogenicity in vivo. As more results of clinical trials carried out so far are gradually becoming available, Dzs may turn out to be safe and well-tolerated therapeutics in humans. Therefore, there is a good chance that we may witness a deoxyribozyme drug reaching the clinic in the near future.

Prospects for nucleic acid-based therapeutics against hepatitis C virus

In this review, we discuss recent advances in nucleic acid-based therapeutic technologies that target hepatitis C virus (HCV) infection. Because the HCV genome is present exclusively in RNA form during replication, various nucleic acid-based therapeutic approaches targeting the HCV genome, such as ribozymes, aptamers, siRNAs, and antisense oligonucleotides, have been suggested as potential tools against HCV. Nucleic acids are potentially immunogenic and typically require a delivery tool to be utilized as therapeutics. These limitations have hampered the clinical development of nucleic acid-based therapeutics. However, despite these limitations, nucleic acid-based therapeutics has clinical value due to their great specificity, easy and large-scale synthesis with chemical methods, and pharmaceutical flexibility. Moreover, nucleic acid therapeutics are expected to broaden the range of targetable molecules essential for the HCV replication cycle, and therefore they may prove to be more effective than existing therapeutics, such as interferon-α and ribavirin combination therapy. This review focuses on the current status and future prospects of ribozymes, aptamers, siRNAs, and antisense oligonucleotides as therapeutic reagents against HCV.

Hepatitis C virus translation inhibitors targeting the internal ribosomal entry site

The internal ribosome entry site (IRES) in the 5' untranslated region (UTR) of the hepatitis C virus (HCV) genome initiates translation of the viral polyprotein precursor. The unique structure and high sequence conservation of the 5' UTR render the IRES RNA a potential target for the development of selective viral translation inhibitors. Here, we provide an overview of approaches to block HCV IRES function by nucleic acid, peptide, and small molecule ligands. Emphasis will be given to the IRES subdomain IIa, which currently is the most advanced target for small molecule inhibitors of HCV translation. The subdomain IIa behaves as an RNA conformational switch. Selective ligands act as translation inhibitors by locking the conformation of the RNA switch. We review synthetic procedures for inhibitors as well as structural and functional studies of the subdomain IIa target and its ligand complexes.

iNOS-targeted 10-23 DNAzyme reduces LPS-induced systemic inflammation and mortality in mice

Sepsis and/or systemic inflammatory response syndrome are leading causes of death in intensive care unit patients. NO is a critical player in the pathogenesis of bacterial sepsis. Several studies demonstrate elevation of iNOS in LPS-induced acute inflammatory responses and mortality; however, the effectiveness of its therapeutic suppression in systemic inflammation is largely controversial. Earlier, we have reported that DNAzymes specific to iNOS mRNA efficiently suppress iNOS expression in LPS-stimulated J774 murine macrophages. In the present study, we explored the effects of two of these DNAzymes in BALB/c mice model of LPS-induced lethal systemic inflammation. Experimental animal groups receiving previous injections of iNOS-specific DNAzyme (100 microg, i.p.) showed significantly reduced mortality. Total cell counts of peritoneal lavage and histopathological studies of tissues demonstrated substantial reduction in the leukocytic infiltration and edema in DNAzyme-treated mice. In addition, DNAzyme-injected animals displayed significantly decreased IL-12 serum level, whereas the levels of IL-1[beta], IFN-[gamma], and TNF-[alpha] also declined to a great extent. DNAzyme treatment resulted in significantly reduced NO levels in serum and peritoneal lavage, confirming functional suppression of iNOS gene in LPS-injected mice. These DNAzymes were also able to limit excessive NO production by cytokine and LPS co-challenges in cultured peritoneal macrophages from DNAzyme-treated mice. Estimation of iNOS mRNA and protein expression in the peritoneal macrophages of DNAzyme-administered animals further confirmed the iNOS gene knockdown. All these results indicated that iNOS-specific DNAzymes reduce inflammatory responses and enhance survival in murine model of LPS-induced lethal systemic inflammation.

Suppression of hepatitis C virus genome replication in cells with RNA-cleaving DNA enzymes and short-hairpin RNA

A class of antisense oligodeoxyribozymes, known as the 10-23 DNA enzymes (DNAzyme), has been shown to efficiently cleave target RNA at purine-pyrimidine junctions in vitro. Herein we have utilized a strategy to identify accessible cleavage sites for DNAzyme in the target RNA, the hepatitis C virus nonstructural gene 3 (HCV NS3) RNA that encodes viral helicase and protease, from a pool of randomized DNAzyme library. The screening procedure identified 18 potential cleavage sites in the target RNA. Corresponding DNAzymes were constructed for the selected target sites and were tested for RNA cleavage in vitro. Using positively charged dendrimer nanoparticles, the target RNA-cleaving DNAzymes that are 31-mer oliogonucleotides are delivered into the human hepatoma cells harboring the HCV subgenomic replicon RNA. DNAzymes introduced into the cells efficiently inhibited HCV RNA replication by reducing the expression of HCV NS3. In addition, we designed short-hairpin RNA (shRNA) that targets the same cleavage site for the selected DNAzyme and confirmed that the shRNA also inhibited HCV NS3 gene expression in the HCV replicon cells. These selected DNAzyme and shRNA may be a viable therapeutic intervention to inhibit HCV replication in hepatic cells. We suggest that the method used in this study can be applicable for identification of available sites in any target RNA for antisense oligonucleotides and siRNAs.

Silencing of TNF-alpha receptors coordinately suppresses TNF-alpha expression through NF-kappaB activation blockade in THP-1 macrophage

Persistently elevated level of TNF-alpha has been implicated in several inflammatory disorders, however, its autocrine production through TNF-alpha receptors signaling is poorly understood. Here we report that simultaneous silencing of TNF-receptors, R1 and R2 by DNAzyme or siRNA suppressed TNF-alpha expression more efficiently than silencing them individually in lipopolysaccharides (LPS) stimulated THP-1 macrophages. Co-silencing of TNF-receptors also inhibited TNF-alpha induced NF-kappaB activation to a higher extent. It was further observed that NF-kappaB inhibitor but not c-Jun N-terminal kinase inhibitor (SP600125) suppressed TNF-alpha expression. All these results suggest that TNF-alpha expression is regulated by synergistic signaling of TNF receptors through downstream NF-kappaB activation.