SMTRI: A deep learning-based web service for predicting small molecules that target miRNA-mRNA interactions

Huan Xiao, Yihao Zhang, Xin Yang, Sifan Yu, Ziqi Chen, Aiping Lu, Zongkang Zhang*, Ge Zhang*, Bao-Ting Zhang*

*Corresponding author for this work

Research output: Contribution to journalJournal articlepeer-review

1 Citation (Scopus)

Abstract

Mature microRNAs (miRNAs) are short, single-stranded RNAs that bind to target mRNAs and induce translational repression and gene silencing. Many miRNAs discovered in animals have been implicated in diseases and have recently been pursued as therapeutic targets. However, conventional pharmacological screening for candidate small-molecule drugs can be time-consuming and labor-intensive. Therefore, developing a computational program to assist mature miRNA-targeted drug discovery in silico is desirable. Our previous work (https://doi.org/10.1002/advs.201903451) revealed that the unique functional loops formed during Argonaute-mediated miRNA-mRNA interactions have stable structural characteristics and may serve as potential targets for small-molecule drug discovery. Developing drugs specifically targeting disease-related mature miRNAs and their target mRNAs would avoid affecting unrelated ones. Here, we present SMTRI, a convolutional neural network-based approach for efficiently predicting small molecules that target RNA secondary structural motifs formed by interactions between miRNAs and their target mRNAs. Measured on three additional testing sets, SMTRI outperformed state-of-the-art algorithms by 12.9%–30.3% in AUC and 2.0%–18.4% in accuracy. Moreover, four case studies on the published experimentally validated RNA-targeted small molecules also revealed the reliability of SMTRI.
Original languageEnglish
Article number102303
Number of pages10
JournalMolecular Therapy - Nucleic Acids
Volume35
Issue number3
DOIs
Publication statusPublished - 10 Sept 2024

Scopus Subject Areas

  • Drug Discovery
  • Molecular Medicine

User-Defined Keywords

  • MT: Bioinformatics
  • convolutional neural network
  • deep learning
  • drug discovery
  • mRNA
  • microRNA
  • small molecule
  • web server

Fingerprint

Dive into the research topics of 'SMTRI: A deep learning-based web service for predicting small molecules that target miRNA-mRNA interactions'. Together they form a unique fingerprint.

Cite this