Screening strategies for identifying RNA- and ribonucleoprotein-targeted compounds

Design, synthesis and characterization of aryl bis-guanyl hydrazones as RNA binders of C9orf72 G4C2 extended repeats

Expanded G4C2 repeats derived from mutations of the C9orf72 gene are causative factors in amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) patients, leading to multiple pathological events. Bis thiophene para dinicotinimidamide 2a was reported to preferentially stabilize G-quadruplex G4C2 RNA structures at sub-micromolar concentrations. We replaced its amidine groups with BBB-compliant guanyl hydrazones, and carried out scaffold variations to improve water solubility. An eight-membered array was built around bis-thiophene- (4b-6a), bis-oxazole- (7b), diphenylurea diamide- (8b) and phenyldioxy ditriazolephenyl scaffolds (9a,b). Biological profiling of the array identified 4b as a promising, drug-like hit, active in cellular assays on ALS patient-derived cells.

19F NMR in RNA structural biology: exploring structures, dynamics, and small molecule interactions

RNA molecules play essential roles in numerous biological pathways, making them attractive targets for drug discovery. Despite the challenges in developing small molecules targeting RNA, the success in developing compounds that modulate RNA function underscores its therapeutic potential. 19F NMR spectroscopy has emerged as a powerful tool in structural biology and drug discovery, particularly for studying macromolecular structures and ligand interactions. As RNA continues to gain prominence as a drug target, 19F NMR is expected to play a pivotal role in advancing RNA-focused drug discovery. This review describes the diverse applications of 19F NMR in RNA biology, including its use in characterizing RNA structures, probing molecular dynamics, identifying small-molecule binders, and investigating interaction mechanisms of small-molecule ligands. By providing detailed structural and ligand binding insights, 19F NMR will facilitate the discovery of RNA-targeting therapeutics and deepen our understanding of RNA modulatory mechanisms.

Targeting and engineering biomarkers for prostate cancer therapy

Prostate cancer (PCa) is the second most commonly occurring cancer among men worldwide. Although the clinical management of PCa has significantly improved, a number of limitations have been identified in both early diagnosis and therapeutic treatment. Because multiple studies show that prostate-specific antigen (PSA) screening frequently results in overdiagnosis and overtreatment, the use of PSA alone as a diagnostic marker for PCa screening has been controversial. For individuals with locally advanced or metastatic PCa, androgen deprivation therapy (ADT) is the standard initially successful treatment; nonetheless, the majority of patients will eventually develop lethal metastatic castration-resistant prostate cancer (CRPC). Alternative treatment options, including chemo-, immuno-,or radio-therapy, can only prolong the survival of CRPC patients for several months with the most developing resistance. Considering this background, there is an urgent need to discuss about selective prostate-specific biomarkers that can predict clinically relevant PCa diagnosis and to develop biomarker-driven treatments to counteract CRPC. This review addresses several PCa-specific biomarkers that will assist physicians in determining which patients are at risk of having high-grade PCa, focusing on the clinical relevance of these biomarker-based tests among PCa patients. Secondly, this review highlights the effective use of these markers as drug targets to develop precision medicine or targeted therapies to counteract CRPC. Altogether, translating this biomarker-based research into the clinic will pave the way for the effective execution of personalized therapies for the benefit of healthcare providers, the biopharmaceutical industry, and patients.

Molecular insights into de novo small-molecule recognition by an intron RNA structure

Despite the promise of vastly expanding the druggable genome, rational design of RNA-targeting ligands remains challenging as it requires the rapid identification of hits and visualization of the resulting cocomplexes for guiding optimization. Here, we leveraged high-throughput screening, medicinal chemistry, and structural biology to identify a de novo splicing inhibitor against a large and highly folded fungal group I intron. High-resolution cryoEM structures of the intron in different liganded states not only reveal molecular interactions that rationalize experimental structure-activity relationship but also shed light on a unique strategy whereby RNA-associated metal ions and RNA conformation exhibit exceptional plasticity in response to small-molecule binding. This study reveals general principles that govern RNA-ligand recognition, the interplay between chemical bonding specificity, and dynamic responses within an RNA target.

DRLiPS: a novel method for prediction of druggable RNA-small molecule binding pockets using machine learning

Ribonucleic Acid (RNA) is the central conduit for information transfer in the cell. Identifying potential RNA targets in disease conditions is a challenging task, given the vast repertoire of functional non-coding RNAs in a human cell. A potential druggable target must satisfy several criteria, including disease association, cellular accessibility, binding pockets for drug-like molecules, and minimal cross-reactivity. While several methods exist for prediction of druggable proteins, they cannot be repurposed for RNAs due to fundamental differences in their binding modality. Taking all these constraints into account, a new structure-based model, Druggable RNA-Ligand binding Pocket Selector (DRLiPS), is developed here to predict binding site-level druggability of any given RNA target. A novel strategy for sampling negative binding sites in RNA structures using three parallel approaches is demonstrated here to improve model specificity: backbone motif search, exhaustive pocket prediction, and blind docking. An external blind test dataset has also been curated to showcase the model's generalizability to both experimental and modelled apo state RNA structures. DRLiPS has achieved an F1-score of 0.70, precision of 0.61, specificity of 0.89, and recall of 0.73 on this external test dataset, outperforming two existing methods, DrugPred_RNA and RNACavityMiner. Further analysis indicates that the features selected for model-building generalize well to both apo and holo states with a backbone RMSD tolerance of 3 Å. It can also predict the effect of binding site single point mutations on druggability, which can aid in optimizing synthetic RNA aptamers for small molecule recognition. The DRLiPS model is freely accessible at https://web.iitm.ac.in/bioinfo2/DRLiPS/.

On the Power and Challenges of Atomistic Molecular Dynamics to Investigate RNA Molecules

RNA molecules play a vital role in biological processes within the cell, with significant implications for science and medicine. Notably, the biological functions exerted by specific RNA molecules are often linked to the RNA conformational ensemble. However, the experimental characterization of such three-dimensional RNA structures is challenged by the structural heterogeneity of RNA and by its multiple dynamic interactions with binding partners such as small molecules, proteins, and metal ions. Consequently, our current understanding of the structure-function relationship of RNA molecules is still limited. In this context, we highlight molecular dynamics (MD) simulations as a powerful tool to complement experimental efforts on RNAs. Despite the recognized limitations of current force fields for RNA MD simulations, examining the dynamics of selected RNAs has provided valuable functional insights into their structures.

Advancements in clinical RNA therapeutics: Present developments and prospective outlooks

RNA molecules have emerged as promising clinical therapeutics due to their ability to target "undruggable" proteins or molecules with high precision and minimal side effects. Nevertheless, the primary challenge in RNA therapeutics lies in rapid degradation and clearance from systemic circulation, the inability to traverse cell membranes, and the efficient intracellular delivery of bioactive RNA molecules. In this review, we explore the implications of RNAs in diseases and provide a chronological overview of the development of RNA therapeutics. Additionally, we summarize the technological advances in RNA-screening design, encompassing various RNA databases and design platforms. The paper then presents an update on FDA-approved RNA therapeutics and those currently undergoing clinical trials for various diseases, with a specific emphasis on RNA medicine and RNA vaccines.

An Encodable Scaffold for Sequence-Specific Recognition of Duplex RNA

RNA, unlike DNA, folds into a multitude of secondary and tertiary structures. This structural diversity has impeded the development of ligands that can sequence-specifically target this biomolecule. We sought to develop ligands for double-stranded RNA (dsRNA) segments, which are ubiquitous in RNA tertiary structure. The major groove of double-stranded DNA is sequence-specifically recognized by a range of dimeric helical transcription factors, including the basic leucine zippers (bZIP) and basic helix-loop-helix (bHLH) proteins; however, such simple structural motifs are not prevalent in RNA-binding proteins. We interrogated the high-resolution structures of DNA and RNA to identify requirements for a helix fork motif to occupy dsRNA major grooves akin to dsDNA. Our analysis suggested that the rigidity and angle of approach of dimeric helices in bZIP/bHLH motifs are not ideal for the binding of dsRNA major grooves. This investigation revealed that the replacement of the leucine zipper motifs in bHLH proteins with synthetic crosslinkers would allow recognition of dsRNA. We show that a model bHLH DNA-binding motif does not bind dsRNA but can be reengineered as an RNA ligand. Based on this hypothesis, we rationally designed a miniature synthetic crosslinked helix fork (CHF) as a generalizable proteomimetic scaffold for targeting dsRNA. We evaluated several CHF constructs against a set of RNA and DNA hairpins to probe the specificity of the designed construct. Our studies reveal a new class of proteomimetics as an encodable platform for sequence-specific recognition of dsRNA.

Study of an RNA-Focused DNA-Encoded Library Informs Design of a Degrader of a r(CUG) Repeat Expansion

A solid-phase DNA-encoded library (DEL) was studied for binding the RNA repeat expansion r(CUG)^exp, the causative agent of the most common form of adult-onset muscular dystrophy, myotonic dystrophy type 1 (DM1). A variety of uncharged and novel RNA binders were identified to selectively bind r(CUG)^exp by using a two-color flow cytometry screen. The cellular activity of one binder was augmented by attaching it with a module that directly cleaves r(CUG)^exp. In DM1 patient-derived muscle cells, the compound specifically bound r(CUG)^exp and allele-specifically eliminated r(CUG)^exp, improving disease-associated defects. The approaches herein can be used to identify and optimize ligands and bind RNA that can be further augmented for functionality including degradation.

Protein-Based Virtual Screening Tools Applied for RNA-Ligand Docking Identify New Binders of the preQ1-Riboswitch

Targeting RNA with small molecules is an emerging field. While several ligands for different RNA targets are reported, structure-based virtual screenings (VSs) against RNAs are still rare. Here, we elucidated the general capabilities of protein-based docking programs to reproduce native binding modes of small-molecule RNA ligands and to discriminate known binders from decoys by the scoring function. The programs were found to perform similar compared to the RNA-based docking tool rDOCK, and the challenges faced during docking, namely, protomer and tautomer selection, target dynamics, and explicit solvent, do not largely differ from challenges in conventional protein-ligand docking. A prospective VS with the Bacillus subtilis preQ₁-riboswitch aptamer domain performed with FRED, HYBRID, and FlexX followed by microscale thermophoresis assays identified six active compounds out of 23 tested VS hits with potencies between 29.5 nM and 11.0 μM. The hits were selected not solely based on their docking score but for resembling key interactions of the native ligand. Therefore, this study demonstrates the general feasibility to perform structure-based VSs against RNA targets, while at the same time it highlights pitfalls and their potential solutions when executing RNA-ligand docking.

Determination of RNA-ligand interactions with the photoaffinity platform PEARL-seq

In the development of therapeutics, it is important to establish engagement of a compound to its intended target and identify other targets it binds to. Methods for demonstrating target engagement in the growing field of RNA-targeted therapeutics are therefore needed. We present a detailed protocol for Photoaffinity Evaluation of RNA Ligation-Sequencing (PEARL-seq), a platform for determining interactions between small molecule ligands and their target RNA(s). PEARL-seq allows detection of binding and crosslinking events with single nucleotide resolution and allows measurement of enrichment of the target RNA relative to all other RNAs. PEARL-seq is a valuable tool in the effort to verify bona fide RNA-ligand interactions.

Targeting Pathogenic DNA and RNA Repeats: A Conceptual Therapeutic Way for Repeat Expansion Diseases

Expansions of short tandem repeats (STRs) in the human genome cause nearly 50 neurodegenerative diseases, which are mostly inheritable, nonpreventable and incurable, posing as a huge threat to human health. Non-B DNAs formed by STRs are thought to be structural intermediates that can cause repeat expansions. The subsequent transcripts harboring expanded RNA repeats can further induce cellular toxicity through forming specific structures. Direct targeting of these pathogenic DNA and RNA repeats has emerged as a new potential therapeutic strategy to cure repeat expansion diseases. In this conceptual review, we first introduce the roles of DNA and RNA structures in the genetic instabilities and pathomechanisms of repeat expansion diseases, then describe structural features of DNA and RNA repeats with a focus on the tertiary structures determined by X-ray crystallography and solution nuclear magnetic resonance spectroscopy, and finally discuss recent progress and perspectives of developing chemical tools that target pathogenic DNA and RNA repeats for curing repeat expansion diseases.

Pharmacophore-Based Discovery of Viral RNA Conformational Modulators

New RNA-binding small-molecule scaffolds are needed to unleash the pharmacological potential of RNA targets. Here we have applied a pharmacophore-based virtual screening approach, seldom used in the RNA recognition field, to identify novel conformational inhibitors of the hepatitis C virus internal ribosome entry site. The conformational effect of the screening hits was assessed with a fluorescence resonance energy transfer assay, and the affinity, specificity, and binding site of the ligands were determined using a combination of fluorescence intensity and NMR spectroscopy experiments. The results indicate that this strategy can be successfully applied to discover RNA conformational inhibitors bearing substantially less positive charge than the reference ligands. This methodology can potentially be accommodated to other RNA motifs of pharmacological interest, facilitating the discovery of novel RNA-targeted molecules.

The multiple molecular dimensions of long noncoding RNAs that regulate gene expression and tumorigenesis

PURPOSE OF REVIEW

LncRNAs are emerging as key regulators of gene expression and they ensure homeostasis during cell differentiation and development, replication, and adaptation to the environment. Because of their key central role in regulating the biology of living cells, it is crucial to characterize how lncRNAs function at the genetic, transcriptomic, and mechanistic level.

RECENT FINDINGS

The low endogenous abundance and high molecular complexity of lncRNAs pose unique challenges for their characterization but new methodological advances in biochemistry, biophysics and cell biology have recently made it possible to characterize an increasing number of these transcripts, including oncogenic and tumor suppressor lncRNAs. These recent studies specifically address important issues that had remained controversial, such as the selectivity of lncRNA mechanisms of action, the functional importance of lncRNA sequences, secondary and tertiary structures, and the specificity of lncRNA interactions with proteins.

SUMMARY

These recent achievements, coupled to population-wide medical and genomic approaches that connect lncRNAs with human diseases and to recent advances in RNA-targeted drug development, open unprecedented new perspectives for exploiting lncRNAs as pharmacological targets or biomarkers to monitor and cure cancer, in addition to metabolic, developmental and cardiovascular diseases.

Small Molecule Drugs Targeting Non-Coding RNAs as Treatments for Alzheimer's Disease and Related Dementias

Despite the enormous burden of Alzheimer's disease and related dementias (ADRD) on patients, caregivers, and society, only a few treatments with limited efficacy are currently available. While drug development conventionally focuses on disease-associated proteins, RNA has recently been shown to be druggable for therapeutic purposes as well. Approximately 70% of the human genome is transcribed into non-protein-coding RNAs (ncRNAs) such as microRNAs, long ncRNAs, and circular RNAs, which can adopt diverse structures and cellular functions. Many ncRNAs are specifically enriched in the central nervous system, and their dysregulation is implicated in ADRD pathogenesis, making them attractive therapeutic targets. In this review, we first detail why targeting ncRNAs with small molecules is a promising therapeutic strategy for ADRD. We then outline the process from discovery to validation of small molecules targeting ncRNAs in preclinical studies, with special emphasis on primary high-throughput screens for identifying lead compounds. Screening strategies for specific ncRNAs will also be included as examples. Key challenges-including selecting appropriate ncRNA targets, lack of specificity of small molecules, and general low success rate of neurological drugs and how they may be overcome-will be discussed throughout the review.