Antiviral RNAi: How to Silence Viruses (original) (raw)

RNAi therapeutics: an antiviral strategy for human infections

Current Opinion in Pharmacology, 2020

Gene silencing induced by RNAi represents a promising antiviral development strategy. This review will summarise the current state of RNAi therapeutics for treating acute and chronic human virus infections. The gene silencing pathways exploited by RNAi therapeutics will be described and include both classic RNAi, inducing cytoplasmic mRNA degradation post-transcription and novel RNAi, mediating epigenetic modifications at the transcription level in the nucleus. Finally, the challenge of delivering gene modifications via RNAi will be discussed, along with the unique characteristics of respiratory versus systemic administration routes to highlight recent advances and future potential of RNAi antiviral treatment strategies.

RNA interference for antiviral therapy

The Journal of Gene Medicine, 2006

Silencing gene expression through a process known as RNA interference (RNAi) has been known in the plant world for many years. In recent years, knowledge of the prevalence of RNAi and the mechanism of gene silencing through RNAi has started to unfold. It is now believed that RNAi serves in part as an innate response against invading viral pathogens and, indeed, counter silencing mechanisms aimed at neutralizing RNAi have been found in various viral pathogens. During the past few years, it has been demonstrated that RNAi, induced by specifically designed double-stranded RNA (dsRNA) molecules, can silence gene expression of human viral pathogens both in acute and chronic viral infections. Furthermore, it is now apparent that in in vitro and in some in vivo models, the prospects for this technology in developing therapeutic applications are robust. However, many key questions and obstacles in the translation of RNAi into a potential therapeutic platform still remain, including the specificity and longevity of the silencing effect, and, most importantly, the delivery of the dsRNA that induces the system. It is expected that for the specific examples in which the delivery issue could be circumvented or resolved, RNAi may hold promise for the development of gene-specific therapeutics. Copyright  2006 John Wiley & Sons, Ltd. Keywords acute viral infection; chronic viral infection RNA interference; antiviral therapy; gene therapy Inhibition of viral transcription by siRNAs After entering the target cells, the virus has to transcribe its genome. In order to do so, the viruses use the host cell machinery, and many viruses also use their own

RNAi Biology, Mechanisms and Therapeutics: Tiny Key Player in Vast Territory

RNA interference (RNAi) is a sequence specific gene silencing process that holds promise for treatment of wide ranging diseases. Data obtained through high-throughput technologies has provided substantial evidence regarding potential of RNAi as an effective technique for knocking down the target genes expression levels, for a better and detailed understanding of intracellular signaling cascades. It is becoming sequentially more understandable that systematically silenced genes using large rationally designed libraries targeting many thousands of genes on a genome-wide scale has provided an innovative functional genomics approach for a deeper and finer knowledge of oncogenic transformation and cell behaviour. It is appropriate to highlight that Sirna Therapeutics (September 2004) and Acuity Pharmaceuticals (August 2004) have registered Investigational New Drug applications with the US FDA for initiation of clinical trials in patients with age-related macular degeneration using modified siRNA molecules. RNAi strategies attracted enormous interest to the phenomena of inhibition of specific viral replications in recent years. This underpinning technology also faces various challenges due to its toxic effects and its delivery to targeted cells. Our understandings of RNAi based phenomena have direct significance for disease etiology and treatment, in addition to fundamental cellular biology. For successive clinical feasibility to tackle human pathogenic viruses, designing of RNAi therapies await further future investigations.

RNA interference against viruses: strike and counterstrike

Nature Biotechnology, 2007

RNA interference (RNAi) is a conserved sequence-specific, gene-silencing mechanism that is induced by double-stranded RNA. RNAi holds great promise as a novel nucleic acid-based therapeutic against a wide variety of diseases, including cancer, infectious diseases and genetic disorders. Antiviral RNAi strategies have received much attention and several compounds are currently being tested in clinical trials. Although induced RNAi is able to trigger profound and specific inhibition of virus replication, it is becoming clear that RNAi therapeutics are not as straightforward as we had initially hoped. Difficulties concerning toxicity and delivery to the right cells that earlier hampered the development of antisense-based therapeutics may also apply to RNAi. In addition, there are indications that viruses have evolved ways to escape from RNAi. Proper consideration of all of these issues will be necessary in the design of RNAi-based therapeutics for successful clinical intervention of human pathogenic viruses.

Rna Interference as Antiviral Therapy: Dream or Reality?

VIRUS Reviews & Research, 2013

Soon aft er discovery of RNA interference (RNAi), its potential as eff ective antiviral therapy was recognized. Since then RNAi has been variously exploited for antiviral purposes which could eff ectively block viral replication in vitro. For in vivo use, however, delivery issue, toxicity, RNAi suppression and viral escape are still major hurdles. Here, we provide an overview of the RNAi strategy and review the approaches that have been developed to surpass the obstacles and to achieve targeted gene silencing for antiviral and other therapies.

A status report on RNAi therapeutics

Silence, 2010

Fire and Mello initiated the current explosion of interest in RNA interference (RNAi) biology with their seminal work in Caenorhabditis elegans. These observations were closely followed by the demonstration of RNAi in Drosophila melanogaster. However, the full potential of these new discoveries only became clear when Tuschl and colleagues showed that 21-22 bp RNA duplexes with 3" overhangs, termed small interfering (si)RNAs, could reliably execute RNAi in a range of mammalian cells. Soon afterwards, it became clear that many different human cell types had endogenous machinery, the RNA-induced silencing complex (RISC), which could be harnessed to silence any gene in the genome. Beyond the availability of a novel way to dissect biology, an important target validation tool was now available. More importantly, two key properties of the RNAi pathway -sequence-mediated specificity and potency -suggested that RNAi might be the most important pharmacological advance since the advent of protein therapeutics. The implications were profound. One could now envisage selecting disease-associated targets at will and expect to suppress proteins that had remained intractable to inhibition by conventional methods, such as small molecules. This review attempts to summarize the current understanding on siRNA lead discovery, the delivery of RNAi therapeutics, typical in vivo pharmacological profiles, preclinical safety evaluation and an overview of the 14 programs that have already entered clinical practice.

Virus Reviews and Research RNA INTERFERENCE AS ANTIVIRAL THERAPY: DREAM OR REALITY

The Progress and Promise of RNA MedicineAn Arsenal of Targeted Treatments

In the last decade, there has been a shift in research, clinical development, and commercial activity to exploit the many roles of RNA in physiology for use in medicine. With the rapid success in the development of lipid-RNA nanoparticles for mRNA vaccines against COVID-19 and with several approved RNA-based drugs, RNA has catapulted to the forefront of drug research. With diverse functions beyond the role of mRNA in producing antigens or therapeutic proteins, many classes of RNA serve a regulatory role in cells and tissues. These RNAs have potential as new therapeutics, with the RNA itself serving as either a drug or a target. These new types of RNA drugs require a plethora of modification chemistries to improve their therapeutic benefit. We describe the current state of the art for RNA medicine. Using the CAS Content Collection data, we examine the publication trends covering the roles of RNA in the cell, the application of RNA in medicine, and the use of chemical modifications and nanotechnology to deliver effective RNA pharmaceuticals to their cellular targets. This review reveals the sustained global effort that propelled this field to the cusp of realization for novel medical applications of RNA in many diseases. It serves as an easy-to-understand overview so that scientists from many different disciplines can appreciate the current state of the field of RNA medicine and join in solving the remaining challenges for fulfilling its potential. ncRNAs, in contrast to mRNA, are the final functional gene products. Although it was thought initially that ncRNAs were nonfunctional junk RNA, in the 1950s, in the same paper that introduced the phrase "Central Dogma", Francis Crick correctly hypothesized that the ncRNA might function in the translation of mRNA into protein. 84 In 1955, George Palade identified ribosomes as a small particulate component of the cytoplasm that contains RNA, and in 1965, Robert Holley purified a tRNA from yeast and determined the structure. 85, 86 In the last half-century, many types of ncRNA with various functions have been identified; many are involved in regulating transcription and protein expression in the cell. 87-94 rRNA, which constitutes up to 80% of the RNA in an active cell, comprises three rRNAs (the 5S, 5.8S, and 28S) complexed with many proteins to form the large subunit of the ribosome and one rRNA (the 18S) complexed with proteins to form the small subunit of the ribosome. There are also two mitochondrial rRNA genes (the 12S and 16S) which, along with many proteins, form the mitochondrial ribosome. rRNA in the ribosome, acting as a ribozyme, catalyzes peptide bond formation between two amino acids. Synthesis of the large amount of rRNA occurs in the nucleolus, a heterochromatic region found in most nuclei. 32, 33 tRNA, which makes up 10-15% of the RNA in the cell, translates the mRNA codon sequence for each amino acid. The many different tRNAs, which are usually 75-95 nucleotides, all fold into very similar three-dimensional structures. The 3D structure exposes three unpaired nucleotides that serve as the anti-codon to base pair with the mRNA. Specific amino acids are covalently bound to a tRNA by aminoacyl tRNA synthetases. The specificity between the anti-codon and the bound amino acid is the basis of translation. Each tRNA anticodon can bind to several different mRNA codons. This pairing is based on the wobble rules for the third nucleotide position of the anti-codon, which is often posttranscriptionally modified to allow for wobble-pairing. Common modifications at the third position include 5-methyl-2-thiouridine, 5-methyl-2'-O-methyluridine, 2'-O-methyluridine, 5-methyluridine, 5hydroxyuridine, hypoxanthine, and lysidine. 32, 33 snRNAs (̴ 150 nucleotides) are components of the small nuclear ribonucleoproteins (snRNPs) of the spliceosome. They act as catalysts that splice mRNA into its mature form and they are important in the selection of alternative splicing sequences. 34-36 snoRNAs (60-300 nucleotides) are bound to four core proteins and act as guides to correctly target modifications for the maturation of rRNA. They comprise two classes of RNA. C/D snoRNAs participate in the 2-methylation of targeted nucleotides, while H/ACA snoRNAs participate in the modification of uridine to pseudouridine. They help guide the protein to the specific target, rather than catalyzing the reaction directly. As participants in rRNA maturation, snoRNAs are found in the nucleolus. 35, 37-44 9 siRNAs are products of double-stranded lncRNAs (e.g., hairpin lncRNA) and are central to RNA interference, which negatively regulates gene expression. Double-stranded RNA (dsRNA), either from genomic lncRNA or dsRNA viruses, is recognized and cleaved by the endonuclease Dicer into 20-24 base-pair sections with short overhangs on both ends. These siRNAs bind the Argonaute protein to form the pre-RISC (RNA-induced silencing complex). Argonaute selects the less thermodynamically stable strand of the siRNA and releases the other strand to form the mature RISC. RISC recognizes mRNA complementary to the single-stranded siRNA, and the Argonaute endonuclease cuts this targeted mRNA, thereby downregulating the gene product. The binding of a RISC to a target mRNA also prevents efficient ribosome binding and translation, further downregulating the gene product. Active RISCs may also affect the transcription of target genes by inducing chromatin reorganization through epigenetic modifications. This can be a defense mechanism against dsRNA viruses or an endogenous generegulatory mechanism. 59-70 miRNAs are closely related to siRNAs but are formed from pri-miRNAs, which are long, imperfectly paired hairpin RNA transcripts. The pri-miRNA is processed first by Drosha nuclease into a ̴ 70-nucleotide imperfectly-paired hairpin pre-miRNA that is then, like siRNA, processed by Dicer to produce the 21-23 bp, mature, double-stranded miRNA that binds to Argonaute to form the RISC. Alternatively, some miRNAs are made from introns in mRNAs. After splicing, that intron is a pre-miRNA that is processed by Dicer to form a RISC. miRNAs form negative gene regulatory networks and intronic miRNAs may regulate and balance potentially competing pathways. 52-58 piRNAs, like siRNA and miRNA, negatively regulate gene expression, but they interact with the Piwi class of Argonaute proteins. Unlike siRNA and miRNA, piRNAs (24-31 nucleotides) are produced from long, single-stranded RNA transcripts through an uncharacterized Dicer-independent mechanism. Mature piRNAs bind to Piwi proteins to form RISCs that act primarily as epigenetic regulators of transposons (genetic elements that move around the genome) but may also regulate transposons posttranscriptionally through the ping-pong pathway. 3, 4, 71-77 saRNA, like siRNA, is a ̴ 21-bp dsRNA long that interacts with Argonaute proteins to form a RISC. Unlike siRNA, saRNA upregulates target gene expression by an unknown mechanism, perhaps activating transcription by targeting the promoter region of the gene. saRNA may be produced endogenously or artificially to strongly activate the target gene. 5, 95-101

Antiviral RNAi: How to Silence Viruses (original) (raw)

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