The past twenty years have seen an explosion of interest in the structure and function of RNA and DNA. While some 80% of the human genome is transcribed into RNA, just ~3% of those transcripts code for protein sequences. Here, we discuss our group’s efforts to target RNA and DNA with drug-like small molecules using a small-molecule microarray (SMM) screening platform and the molecular basis for these interactions.

As part of our efforts to improve small molecule targeting strategies and gain fundamental insights into small molecule:RNA recognition, we have analyzed patterns in both RNA-biased small molecule chemical space and RNA topological space privileged for differentiation. We have applied these principles to functionally modulate conformations of the 3’-triple helix of the long noncoding RNA MALAT1, an enterovirus (EV71) IRES structure, and regulatory RNA in SARS-CoV-2.

Anima Biotech has developed Translation Control Therapeutics, a novel approach for the discovery of small molecules that selectively control mRNA translation against hard targets and undruggable proteins. With this technology that emits light pulses from ribosomes, we visualize and analyze the kinetics of mRNA translation and identify selective translation modulators. Anima's lead compounds do not directly bind mRNA or degrade it but rather intervene by regulating mRNA translation in a tissue selective or disease-specific manner.

Our laboratory has targeted RNA with small molecules for sixteen years. First we define fundamental features of molecular recognition. This information is mined against the human transcriptome to identify disease-causing RNAs with motifs bound by small molecules, using an approach termed Inforna. These compounds can be selectively and potently bioactive and can be designed into molecules that facilitate RNA degradation by recruiting ribonucleases to catalytically and sub-stoichiometrically degrade disease-causing RNAs.

Utilizing small molecules to modulate splicing has emerged as a successful therapeutic approach to regulating protein expression. Here, three diseases where small-molecule splicing modulators can be utilized are described: spinal muscular atrophy; familial dysautonomia; and Huntington’s disease. For each of these indications, I will discuss the correlation between pharmacokinetics and pharmacodynamics, as well as the correlation between pharmacodynamics and efficacy.

The recent approval of an RNA-targeted small molecule for spinal muscular atrophy has re-affirmed the great promise of direct targeting of RNA for accessing previously undruggable targets. Ligand discovery strategies that embrace structural diversity, when coupled with appropriate informatics, phenotypic screening, chemical biology, and medicinal chemistry tools, can lead to the next generation of small molecules targeting RNA. Attend this talk to get insights on current approaches and potential future directions.

RNAs are invariably bound to and often modified by RNA-binding proteins (RBPs), which regulate many aspects of coding and non-coding RNA biology. Disruption of this network of RNA-protein interactions (RPIs) has been implicated in a number of human diseases and targeting RPIs has arisen as a new frontier in RNA-targeted drug discovery. This talk will highlight newly developed technologies for validating and screening RPIs to enable RBP-targeted drug discovery.

The discovery and design of biologically important RNA molecules is outpacing three-dimensional structural characterization. I will describe results from my and Wah Chiu's groups that demonstrate that cryo-electron microscopy can resolve maps of several kinds of RNA-only systems. These maps enable sub-nanometer-resolution coordinate estimation when complemented with multi-dimensional chemical mapping and Rosetta DRRAFTER computational modeling. 

In fragile X syndrome, the most common genetic form of mental retardation, a CGG trinucleotide–repeat expansion adjacent to the fragile X mental retardation 1 (FMR1) gene promoter results in its epigenetic silencing. We have found that FMR1 gene silencing is mediated by the FMR1 mRNA. The FMR1 mRNA contains the transcribed CGG-repeat tract as part of the 5′ untranslated region, which hybridizes to the complementary CGG-repeat portion of the FMR1 gene to form an RNA·DNA duplex. Here we describe how small molecules that bind the CGG-repeat RNA region can prevent FMR1 gene silencing in a model of embryonic development. We also describe a strategy for selectively reversing the epigenetic silencing marks on the FMR1 locus in patient-derived cells. Thus, our data show that an RNA-binding small molecule can selectively control the epigenetic activation state of a single gene in the genome, providing novel therapeutic implications for the treatment of fragile X syndrome.