Exploring Chemical Modifications for siRNA Therapeutics: A Structural and Functional Outlook

Abstract

RNA interference (RNAi) is a post-transcriptional gene silencing mechanism induced by small interfering RNAs (siRNAs) and micro-RNAs (miRNAs), and has proved to be one of the most important scientific discoveries made in the last century. The robustness of RNAi has opened up new avenues in the development of siRNAs as therapeutic agents against various diseases including cancer and HIV. However, there had remained a lack of a clear mechanistic understanding of messenger RNA (mRNA) cleavage mediated by Argonaute2 of the RNA-induced silencing complex (RISC), due to inadequate structural data. The X-ray crystal structures of the Argonaute (Ago)-DNA-RNA complexes reported recently have proven to be a breakthrough in this field, and the structural details can provide guidelines for the design of the next generation of siRNA therapeutics. To harness siRNAs as therapeutic agents, the prudent use of various chemical modifications is warranted to enhance nuclease resistance, prevent immune activation, decrease off-target effects, and to improve pharmacokinetic and pharmacodynamic properties. The focus of this review is to interpret the tolerance of various chemical modifications employed in siRNAs toward RNAi by taking into account the crystal structures and biochemical studies of Ago-RNA complexes. Moreover, the challenges and recent progress in imparting druglike properties to siRNAs along with their delivery strategies are discussed.

Structure - Functions Relations in Small Interfering RNAs

“…At the beginning this approach was proposed as a way to increase nuclease resistance of siRNA in the presence of serum, in the cells and bloodstream [61,62]. The enhancement of nuclease resistance of siRNA by chemical modification not resulting in the drop of its silencing activity represent a complex task, since silencing activity of siRNA is strongly affected by the nature, number and locations within the duplex of chemical modifications [65,76,181]. Despite many works carried out in this area, a general algorithm which allows receiving active nuclease resistant siRNA is not developed yet.…”

Remedial applications of silencing ribonucleic acids and modalities for its delivery to the kidneys - A review

“…Tissues containing silencing RNA may be used in the possible heart transplantation in animal models (Negishi et al, 2008). In comparative studies it was observed that silencing RNA labeled with fluorescent administered rectal and intra-peritoneal significant uptake was observed in the rectal administration after 4 hours of the dosing (Shukla et al, 2009). This study showed that silencing RNA was useful in tissue retaining but proteins were not studied.…”

SMEpred workbench: A web server for predicting efficacy of chemicallymodified siRNAs

“…These include low efficacy of mRNA inhibition, off targets, immunogenicity, low serum stability against the nucleases, cell specific delivery problems, target site recognition, accessibility and its cleavage. [7][8][9] To overcome most of these shortcomings, siRNA molecules are engineered by introducing chemical modifications. 9,10 Natural RNAs comprises of ribonucleotide-moieties, composed of sugar (Ribose), phosphate (phosphodiester bond) and nitrogenous bases Adenine (A), Guanine (G), Cytosine (C), and Uracil (U).…”

“…11 With modifications on these constituent molecules, sphere of their functionality has been enhanced. 8 Numerous studies on chemical modifications directed on siRNAs are reported in the literature aimed to improve their therapeutic potential. 6 Testing different chemical modifications at different positions and their combinations on siRNAs are vast.…”