Hepatitis C virus (HCV) is a global health concern; recent estimates suggest that 2.2 to 3% of the world's population, equivalent to 130 to 170 million individuals, are chronically infected with the virus (13, 31). These patients are at risk of developing debilitating liver diseases such as cirrhosis and hepatocellular carcinoma (1). Furthermore, current models suggest that the burden of HCV-associated disease is set to rise for the next 20 years (6). There is no HCV vaccine; the current standard of care (SOC) involves lengthy treatments with ribavirin and injected pegylated interferon, which exhibit variable efficacies and are associated with severe, and sometimes lifethreatening, side effects. Encouragingly, many direct-acting antiviral (DAA) molecules are in clinical development, and the most advanced (telaprevir and boceprevir) will probably be used to treat HCV-infected patients in 2011 (19,29,42,43,61). However, caution should be employed against overoptimism; attrition rates are high during drug development, and the first drugs will be given in combination with, not instead of, the current SOC. Therefore, the continued development of additional treatments is needed, especially since it is widely acknowledged that to limit the emergence of drug-resistant viral variants, effective therapeutic strategies for HCV will consist of multiple DAAs (50).A multitude of screening campaigns has revealed many diverse and interesting chemical compounds capable of specifically inhibiting HCV RNA replication. Many of these compounds target the HCV-encoded nonstructural (NS) proteins (NS3, NS4A, NS4B, NS5A, and NS5B), which are required for HCV genome synthesis (3, 37). To instigate HCV genome replication, the NS proteins interact with viral genomes and certain host-encoded factors to form multiprotein assemblies termed "replication complexes" (RCs), which are sites of viral RNA synthesis derived from the endoplasmic reticulum (ER) (8,14,45,53). In HCV-infected cells, RCs are juxtaposed to intracellular lipid storage organelles termed lipid droplets (LDs), which are coated with the HCV capsid protein (core) and probably serve as platforms to accept replicated genomes from RCs to initiate virion assembly (26,44,53). Of considerable interest are inhibitors that target the HCV-encoded NS5A protein. These inhibitors were originally discovered from the screening of cells containing HCV subgenomic replicons against libraries of small molecules and were identified as NS5A inhibitors by utilizing a strategy termed "chemical genetics" (12, 32). NS5A-targeting inhibitors are notable for their unprecedented potency in cell-based HCV replication assays: 50% inhibitory concentrations (IC 50 s) in the low-picomolar

The hepatitis C virus (HCV) chronically infects 2% of the world population and effective treatment is limited by long duration and significant side-effects. Here, we describe a novel drug, intended as a “single-shot ” therapy, which expresses three short hairpin RNAs (shRNAs) that simultaneously target multiple conserved regions of the HCV genome as confirmed in vitro by knockdown of an HCV replicon system. Using a recombinant adeno-associated virus (AAV) serotype 8 vector for delivery, comprehensive transduction of hepatocytes was achieved in vivo in a nonhuman primate (NHP) model following a single intravenous injection. However, dose ranging studies performed in 13 NHP resulted in high-expression levels of shRNA from wild-type (wt) Pol III promoters and dose-dependent hepatocellular toxicity, the first demonstration of shRNA-related toxicity in primates, establishing that the hepatotoxicity arises from highly conserved features of the RNA interference (RNAi) pathway. In the second generation drug, each promoter was re-engineered to reduce shRNA transcription to levels that circumvent toxicity but still inhibit replicon activity. In vivo testing of this modified construct in 18 NHPs showed conservation of hepatocyte transduction but complete elimination of hepatotoxicity, even with sustained shRNA expression for 50 days. These data support progression to a clinical study for treatment of HCV infection.

TT-034 (PF-05095808) is a recombinant adeno-associated virus serotype 8 (AAV8) agent expressing three short hairpin RNA (shRNA) pro-drugs that target the hepatitis C virus (HCV) RNA genome. The cytosolic enzyme Dicer cleaves each shRNA into multiple, potentially active small interfering RNA (siRNA) drugs. Using next-generation sequencing (NGS) to identify and characterize active shRNAs maturation products, we observed that each TT-034–encoded shRNA could be processed into as many as 95 separate siRNA strands. Few of these appeared active as determined by Sanger 5′ RNA Ligase-Mediated Rapid Amplification of cDNA Ends (5-RACE) and through synthetic shRNA and siRNA analogue studies. Moreover, NGS scrutiny applied on 5-RACE products (RACE-seq) suggested that synthetic siRNAs could direct cleavage in not one, but up to five separate positions on targeted RNA, in a sequence-dependent manner. These data support an on-target mechanism of action for TT-034 without cytotoxicity and question the accepted precision of substrate processing by the key RNA interference (RNAi) enzymes Dicer and siRNA-induced silencing complex (siRISC).

PF-05095808 is a novel biological agent for chronic hepatitis C virus (HCV) therapy. It comprises a recombinant adenoassociated virus (AAV) DNA vector packaged into an AAV serotype 8 capsid. The vector directs expression of three short hairpin RNAs (shRNAs) targeted to conserved regions of the HCV genome. These shRNAs are processed by the host cell into the small interfering RNAs which mediate sequence-specific cleavage of target regions. For small-molecule inhibitors the key screens needed to assess in vitro activity are well defined; we developed new assays to assess this RNA interference agent and so to understand its therapeutic potential. Following administration of PF-05095808 or corresponding synthetic shRNAs, sequence-specific antiviral activity was observed in HCV replicon and infectious virus systems. To quantify the numbers of shRNA molecules required for antiviral activity in vitro and potentially also in vivo, a universal quantitative PCR (qPCR) assay was developed. The number of shRNA molecules needed to drive antiviral activity proved to be independent of the vector delivery system used for PF-05095808 administration. The emergence of resistant variants at the target site of one shRNA was characterized. A novel RNA cleavage assay was developed to confirm the spectrum of activity of PF-05095808 against common HCV clinical isolates. In summary, our data both support antiviral activity consistent with an RNA interference mechanism and demonstrate the potential of PF-05095808 as a therapeutic agent for chronic HCV infection.

The chemistry of aptamers is largely limited to natural nucleotides, and although modifications of nucleic acids can enhance target aptamer affinity, there has not yet been a technology for selecting...