Strategies for the Design of Drugs Targeting RNA and RNA–Protein Complexes

Abstract

In many steps of gene replication and expression, RNA molecules participate as key players, which renders them attractive targets for therapeutic intervention. While the function of nucleic acids as carriers of genetic material is based on their sequence, a number of important RNAs are involved in processes that depend on the defined three‐dimensional structures of these molecules. As for proteins, numerous complex folds of RNA exist. The development of drugs that bind specifically to RNA folds opens exciting new ways to expand greatly the existing repertoire of protein‐targeted therapeutics. Most functions of RNAs involve interactions with proteins that contain RNA‐binding domains. Effector molecules targeted at RNA may either alter the functional three‐dimensional structure of the nucleic acid, so the interaction with proteins is thereby inhibited or enhanced, or, as interface inhibitors, they may directly prevent the formation of competent RNA–protein complexes. While the same tools used for the design of protein‐targeted drugs may be considered for studying effectors binding to nucleic acids, the differences between proteins and RNAs in the forces which dominate their three‐dimensional folding call for novel drug design strategies. In the present review, I will outline how our rapidly expanding knowledge of RNA three‐dimensional structure and function facilitates rational approaches to develop RNA‐binding compounds. Putative RNA targets for therapeutic intervention will be discussed along with recent advances in understanding RNA–small molecule and RNA–protein interactions.

Selection of RRE RNA binding peptides using a kanamycin antitermination assay

“…Because of its structural plasticity and relative sequence simplicity, the arginine-rich motif has proven to be a versatile framework for identifying novel RNA binders from combinatorial libraries (Harada et al 1996(Harada et al , 1997Tan and Frankel 1998;Barrick et al 2001). Such molecules have been useful for defining new RNA recognition strategies, have provided useful reagents for probing RNA function, and may provide starting points for designing therapeutic inhibitors that target key RNA sites, such as the RRE (Hermann 2000;Cheng et al 2001).…”

Acid–base properties of functionalised tripodal polyamines and their interaction with nucleotides and nucleic acids

“…As an 5 alternative method for estimation of affinity, at least as a comparison of ability of studied molecules to compete for binding with classical intercalators already bound to dspolynucleotides, 25 we have performed ethidium bromide (EB) displacement assays ( Figure S5, ESI † ). 10 The obtained IC 50 = 1.2 -0.15 suggest that affinities of L 4 -L 7 toward ct-DNA and poly A-poly U are comparable to the affinity of EB. Since the structures of L 4 -L 7 do not support intercalation into ds-DNA/RNA as a binding mode but more likely an electrostatic interactions, the obtained IC 50 values 15 cannot be used for accurate calculation of binding constants but only as a measure of high affinity (logKs > 5).…”

“…Table S1, (ESI †). GMT, 10 TMP and UMP show a deprotonation process of the imide nitrogen in the heterocyclic base. 23 AMP and CMP bear a protonation of the nitrogen N1 in the aromatic ring.…”

“…However, T m values > 30 º C are not common for poly A-poly U, thus a possible formation of very stable triple helical polynucleotide (like the ones observed for DNA analogues) 29 cannot be neglected. 10 In order to get insight into the changes of polynucleotide secondary structure induced by small molecule binding, we have chosen Circular Dichroism (CD) spectroscopy. 30 In addition, achiral small molecules can eventually acquire induced CD spectrum (ICD) upon binding to polynucleotides, 15 which could give useful information about modes of interaction.…”

“…Figure S1 (ESI † ) includes the distribution diagram for the species existing in equilibrium for all receptors L 4 -L 7 . The trend of the protonation constants can be largely interpreted in terms of minimization of 10 coulombic repulsion between same sign charges. 17 All ligands L 4 -L 7 present six relatively high basicity constants in agreement with the protonation of the secondary amine nitrogen atoms.…”