Advances in machine-learning approaches to RNA-targeted drug design.

Artif Intell Chem

Department of Physics and Astronomy, Department of Biochemistry, Institute of Data Sciences and Informatics, University of Missouri, Columbia, MO 65211-7010, USA.

Published: June 2024


Category Ranking

98%

Total Visits

921

Avg Visit Duration

2 minutes

Citations

20

Article Abstract

RNA molecules play multifaceted functional and regulatory roles within cells and have garnered significant attention in recent years as promising therapeutic targets. With remarkable successes achieved by artificial intelligence (AI) in different fields such as computer vision and natural language processing, there is a growing imperative to harness AI's potential in computer-aided drug design (CADD) to discover novel drug compounds that target RNA. Although machine-learning (ML) approaches have been widely adopted in the discovery of small molecules targeting proteins, the application of ML approaches to model interactions between RNA and small molecule is still in its infancy. Compared to protein-targeted drug discovery, the major challenges in ML-based RNA-targeted drug discovery stem from the scarcity of available data resources. With the growing interest and the development of curated databases focusing on interactions between RNA and small molecule, the field anticipates a rapid growth and the opening of a new avenue for disease treatment. In this review, we aim to provide an overview of recent advancements in computationally modeling RNA-small molecule interactions within the context of RNA-targeted drug discovery, with a particular emphasis on methodologies employing ML techniques.

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10904028PMC
http://dx.doi.org/10.1016/j.aichem.2024.100053DOI Listing

Publication Analysis

Top Keywords

rna-targeted drug
12
drug discovery
12
machine-learning approaches
8
drug design
8
interactions rna
8
rna small
8
small molecule
8
drug
6
advances machine-learning
4
approaches rna-targeted
4

Similar Publications

Hypertension is the single most important modifiable risk factor for preventable disability and death worldwide and disproportionately affects socially disadvantaged populations. We face a paradox-blood pressure control is low and recent trends suggest it is even declining, despite the availability of inexpensive and effective therapies. A variety of barriers on the system, patient, and healthcare provider side hinder effective drug-based risk factor management.

View Article and Find Full Text PDF

RNA-targeting small molecules represent a transformative frontier in drug discovery, offering novel therapeutic avenues for diseases traditionally deemed undruggable. This review explores the latest advancements in the development of RNA-binding small molecules, focusing on the current obstacles and promising avenues for future research. We highlight innovations in RNA structure determination, including X-ray crystallography, nuclear magnetic resonance spectroscopy, and cryo-electron microscopy, which provide the foundation for rational drug design.

View Article and Find Full Text PDF

In silico screening and experimental validation identify riboflavin as an RNA-targeted antiviral against SARS-CoV-2.

Sci Rep

August 2025

Division of Clinical Research, Center for Emerging Virus Research, National Institute of Infectious Diseases, Korea National Institute of Health, 212 Osongsaengmyeong2-ro, Osong-eup, Heungdeok-gu, Cheongju, 28160, Republic of Korea.

This study explored drug repurposing strategies against conserved RNA structures in the SARS-CoV-2 genome to address viral mutation challenges. Conserved RNA elements were computationally identified by aligning 283 SARS-CoV-2 genomes from Korean patients. RNA secondary structures were predicted using RNAfold and RNAstructure, followed by virtual screening of 11 compounds using the RNALigands database (binding energy threshold: -6.

View Article and Find Full Text PDF

Cardiovascular (CV) diseases continue to cause substantial morbidity and mortality. Risk factors are inadequately controlled, compliance with medication remains suboptimal, and treatments are not sufficient to fully prevent the progression of atherosclerotic CV disease, heart failure, arrhythmias, and valvular heart diseases. An increased understanding of the genetic basis of CV diseases and advances in the technology of therapeutics have led to the development of nucleic acid-based therapies (NATs) for prevention and treatment of CV risk factors and diseases.

View Article and Find Full Text PDF

Circular RNAs (circRNAs) are a class of noncoding RNAs characterized by covalently closed loop structures that confer high stability and diverse regulatory functions. Emerging evidence suggests that circRNAs modulate gene expression by acting as miRNA sponges, interacting with RNA-binding proteins (RBPs), influencing transcription, and serving as translational templates. Their dysregulation has been linked to various diseases, including cancer, cardiovascular, neurodegenerative, and metabolic disorders.

View Article and Find Full Text PDF