Over the past decades, we have witnessed an explosion in discoveries connecting RNAs with human diseases. Consequently, the targeting of RNAs, and more broadly, RNA biology, has emerged as an untapped area of drug discovery. In this lecture, I will discuss methods developed by the Garner Lab for exploring the druggability of cellular RNAs and RNA-protein interactions.

RNA is a versatile molecule and exhibits many diverse functions. Our lab explores approaches and chemistries to study RNA structure and druggability. Using customized affinity-based profiling tools, we study RNA structural folding and small molecule ligand binding. Applying these tools to structured RNA, we determine ligand binding sites with single nucleotide resolution. Lastly, combining our tools with qPCR allows us to measure binding of RNA targeting drugs in live cells.

I will discuss transcriptome-wide methods we have developed to assess defects and RNA binding protein-RNA changes in small molecule-mediated perturbation of systems.

Here, we develop a photo-activatable-competition and chemoproteomic enrichment (PACCE) method for detecting thousands of cysteine sites on proteins displaying RNA-sensitive alterations in probe binding. PACCE is complementary to existing RNA interactome capture methods and enabled functional profiling of canonical RNA-binding domains as well as discovery of moonlighting RNA binding activity in the human proteome. Collectively, we introduce a chemoproteomic platform for proteome-wide quantification of protein-RNA binding activity in living cells.

Small-molecule splicing modifiers to regulate protein expression have emerged as a successful strategy to address certain diseases. Diseases such as spinal muscular atrophy, familial dysautonomia, and Huntington’s disease can be targeted by small-molecule splicing modifiers. The correlation between pharmaceutical properties and pharmacokinetics, pharmacokinetics and pharmacodynamics, and between pharmacodynamics and efficacy will be discussed for select indications.

Our mission at Arrakis is to solve very broadly the problem of how to drug RNA with small molecules. This presentation will provide an update on the platform we have built to achieve that mission and provide early data on specific mRNA targets.

Targeting RNAs and modulating their function could transform drug discovery. An estimated 85% of the ~3 billion base pairs in the human genome are transcribed into RNA, but only ~1.5% of these code for proteins. At Serna Bio we are using an AI-enabled, data-first approach to build the world's first map of the druggable transcriptome. I will discuss some of the challenges of developing and advancing target-specific programs.

This talk will cover recent examples on the development of click-degraders, small molecules that when in proximity can degrade RNA, akin to ribonucleases. Using click-degraders we developed meCLICK-Seq, a powerful method for the study of diverse aspects of cellular RNA methylation. We also developed proximity-driven small molecule RNA degraders to target and degrade SARS-CoV-2 genomes and exert an antiviral effect in disease models.

RNA viruses such as SARS-CoV-2 have highly structured untranslated regions (UTRs), which are vital for viral propagation. These RNA structures are promising antiviral targets. We developed a new class of molecules that target the four-way junction RNA structure named SL5 in the 5’ UTR of the SARS-CoV-2 genome. We optimized the SL5-binding ligand, conjugated it to ribonuclease-recruiting moieties to create active RNA-degrading chimeras, and demonstrated their activities in SARS-CoV-2-infected cells.

Modulating RNA functions emerges as an attractive therapeutic modality in several disease areas. By deploying chemogenomic tools, we identify and validate preclinically human prolyl-tRNA synthetase as a novel target in haematological and solid cancers. Inhibition leads to dose-dependent down-regulation of proline-rich oncogenic transcription factors and signaling molecules with concomitant cancer cell death, reduction in tumor burden, and increased host survival in ex vivo and in vivo systems.

We performed proteomic studies on cells treated with rationally designed CRBN modulators and identified novel molecular glue degraders of a previously “undruggable” RNA binding oncoprotein (RBP). RBP controls the levels of BRAF and EGFR, and its targeted degradation inhibited BRAF-mutant colorectal cancer cell proliferation and tumor growth, either alone or synergistically with BRAF inhibitors.

The Alzheimer’s amyloid precursor-protein and Parkinson’s alpha-synuclein were rigorously shown by our laboratory at MGH to be translationally controlled via the 5’untranslated regions of their mRNAs in neurons, i.e., via uniquely-folded iron-responsive-elements RNA stem-loops. Our new 5’UTR inhibitors limited APP-amyloid and alphasynuclein in the nanomolar range to prevent formation of toxic fibrils in mouse models of PD. We unexpectedly discovered these RNA inhibitors can readily be repurposed to inhibit translation of the replicase in SARS-CoV-2.