The Emerging Role of RNA as a Therapeutic Target for Small Molecules

Abstract

Recent advances in understanding different RNAs and unique features of their biology have revealed a wealth of information. However, approaches to identify small molecules that target these newly discovered regulatory elements have been lacking. The application of new biochemical screening and design-based technologies, coupled with a resurgence of interest in phenotypic screening, has resulted in several compelling successes in targeting RNA. A number of recent advances suggest that achieving the long-standing goal of developing drug-like, biologically active small molecules that target RNA is possible. This review highlights advances and successes in approaches to targeting RNA with diverse small molecules, and the potential for these technologies to pave the way to new types of RNA-targeted therapeutics.

Figure 1

Structure- and Design-Based Approaches for Identifying RNA-Binding Molecules (A) Representative conformers of wild-type HIV-1 TAR RNA (left) used to identify TAR-binding small molecules (right) by virtual screening (Stelzer et al., 2011). (B) Crystal structure of the HCV IRES subdomain IIa RNA in complex with the benzimidazole inhibitor 4 showing the small-molecule-induced change in the interhelical angle of the RNA (left), and structures of the identified HCV translation inhibitors that bind to subdomain IIa (right) (Parsons et al., 2009). (C) Structure of the r(CUG)₆ duplex (left) used to rationally design a highly selective CUG binding ligand 5 based on the triaminotriazine scaffold (right) (Nguyen et al., 2015, Wong et al., 2014). Structures of r(CUG)^exp binding compounds 6 and 7 identified by high-throughput screening efforts are also shown (right) (Childs-Disney et al., 2013, Rzuczek et al., 2015). (D) Representative structure of a three-way junction (left) for which RNA-binding triptycene-based scaffolds such as compound 8 (right) were developed (Barros et al., 2016a). (E) Structure of the SARS-CoV RNA pseudoknot involved in an essential −1 ribosomal frameshift (left) used in a virtual screen to identify a SARS-pseudoknot-binding ligand (right) (Park et al., 2011).

Figure 2

Application of Inforna to the Identification of Small Molecules that Bind to Disease-Associated RNAs A database of RNA motif-small molecule interactions was used to predict compounds that bind to the 1 × 1 nucleotide GG internal loops present in the c9FTD/ALS-associated r(GGGGCC)^exp (top, blue), or to the 1 × 1 nucleotide UU internal loops present in the Dicer and Drosha processing sites of the cancer associated miR-544 hairpin precursor (bottom, red). Structures of validated lead compounds that bind to r(GGGGCC)₈ and the miR-544 hairpin precursor are shown in blue and red, respectively (Haga et al., 2015, Velagapudi et al., 2014).

Figure 3

Fragment-Based Discovery of RNA-Binding Molecules (A) Chemical structures of four TPP riboswitch-binding fragments (left) and the cocrystal structure of TPP riboswitch bound to 16, depicting a rearrangement of G72 (right) (Cressina et al., 2011, Warner et al., 2014). (B) ¹⁹F-NMR fragment-based screening strategy to identify chemically diverse compounds that bind to TERRA (left), in which ¹⁹F-NMR signals are perturbed or broadened by compounds binding. Chemical structures of four representative hits that bind to TERRA₂ are shown on the right. Fluorines are indicated in red (Garavis et al., 2014). (C) Fragment-based screening hit (DPQ) and improved analog that bind to the influenza A promoter RNA. Also shown is a structure of the promoter RNA in complex with DPQ (Bottini et al., 2015, Lee et al., 2014).

Figure 4

Use of Small-Molecule Microarrays to Identify RNA-Binding Molecules (A) Small-molecule microarray screening approach. (B) Structure of a molecule discovered by SMM screening to bind specifically to the HIV TAR hairpin, but not other structural elements of the HIV 5′ UTR (Sztuba-Solinska et al., 2014).

Figure 5

Dynamic Combinatorial Approaches to Identify RNA-Binding Molecules Generic depiction of a dynamic combinatorial chemistry approach (A). Targets for dynamic combinatorial chemistry include both (B) DM1-associated (CUG) repeat RNA and (C) the HIV-1 frameshift-inducing RNA stem loop (Gareiss et al., 2008, Hilimire et al., 2015, Ofori et al., 2014). RBDCL, resin-bound dynamic combinatorial library.

Figure 6

Use of Phenotypic Assays to Identify RNA-Binding Molecules (A) Schematic of a reporter gene assay that utilizes luciferase expression to measure exon 7 exclusion/inclusion in SM2 splicing. Chemical structures of NVS-SM2 and its inactive analog NVS-SM3. Putative binding site of NVS-SM2 within the crystal structure of the U1 snRNP-SMN pre-mRNA with rainbow coloring indicating 5′ (blue) to 3′ (red) (bottom) (Palacino et al., 2015). (B) Depiction of a whole-cell phenotypic screening assay (top left) to identify inhibitors of riboflavin biosynthesis (right). In the absence of riboflavin, ribocil produces a clear zone as a result of growth inhibition. Cocrystal structure of the FMN riboswitch bound to ribocil B (bottom left) (Howe et al., 2015).