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Multivalent Engineered RNA Molecules that Interfere with Hepatitis C Virus Translation and Replication
* 1 , 2 , 1 , * 1
1  Institute of Parasitology and Biomedicine López-Neyra, IPBLN-CSIC, Spain
2  INSERM U1052, Cancer Research Center of Lyon (CRCL), Université Claude-Bernard (UCBL), France

Published: 01 November 2017 by MDPI in 3rd International Electronic Conference on Medicinal Chemistry session ECMC-3

The design of novel and efficient compounds fighting against the highly variable RNA viruses, such as hepatitis C virus (HCV), is a major goal. RNA oligonucleotides have gained great interest as specific molecular tools for inhibiting essential viral processes. The combination of different RNA molecules with proven antiviral activity, each with its own activity and specificity, into a single molecule yields the so-called multivalent compounds, which are promising candidates for the development of new therapeutic strategies. These compounds are chimeric entities with enhanced therapeutic properties. In this work, the previously developed chimeric inhibitor RNA HH363-10 was used as archetype for the development of improved anti-HCV inhibitors. HH363-10 consists of a hammerhead ribozyme domain, targeting the essential internal ribosome entry site (IRES) region in the 5’ end of the HCV genome; and an aptamer RNA molecule, directed against the highly conserved IIIf domain of the IRES. As a result of the application of an in vitro selection process to the RNA pool, which results from the partial randomization of the aptamer-domain sequence of the HH363-10 molecule, 10 new multivalent optimized chimeric antiHCV RNA molecules were selected for further analysis. The aptamer RNA domain was evolved to contain two binding sites: the one mapping the IIIf domain, and a newly acquired targeting site, either to the IRES domain IV (which contains the translation start codon) or the essential linker region between the IRES domains I and II. These chimeric molecules efficiently and specifically interfered with HCV IRES-dependent translation in vitro (with IC50 values in the low µM range). They also inhibited both viral translation and replication in cell culture. These findings highlight the feasibility of using in vitro selection strategies for obtaining improved, multivalent RNA molecules with potential clinical applications.

Keywords: RNA aptamer; hepatitis C virus; IRES; RNA targeting
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