Docking and Molecular Dynamics Simulation‐Based Analysis of Advanced Small‐Molecule Kinase Inhibitors Identified pre‐let‐7 miRNA Binders

TL;DR

This study uses computational and biophysical methods to find FDA-approved kinase inhibitors that bind to pre-let-7 microRNA, suggesting they might have RNA-targeting effects.

Contribution

The study demonstrates that FDA-approved kinase inhibitors can bind to pre-let-7 microRNA, highlighting the need to explore RNA targets for these drugs.

Findings

Several FDA-approved kinase inhibitors showed binding affinity to pre-let-7 microRNA.

Molecular dynamics simulations and docking scores identified top-performing inhibitors.

Microscale thermophoresis validated the strongest SMKI–miRNA interactions.

Abstract

RNAs play crucial roles in various cellular actions, and the uncontrolled expression or improper folding of RNAs is a cause of many diseases. Certain oncogenic phenotypes stem from the overexpression of regulatory microRNAs that contain secondary structural elements. Thus, targeting disease‐related microRNAs with small molecules is a potential therapeutic strategy that has attracted growing interest. To probe the RNA‐binding chemical space held in advanced small‐molecule therapeutics, in this work, we screened the 78 FDA‐approved small‐molecule kinase inhibitors (SMKIs) as representatives of the most advanced kinase inhibitors for their binding affinity with pre‐let‐7 miRNA via a combination of computational methods and biophysical measurement. The best‐ranked SMKIs based on docking scores were subjected to molecular dynamics simulation studies, followed by analysis of different computational parameters. Collectively, it provided reliable information on the binding affinity for the top‐performed SMKI in the formation of SMKI–miRNA complexes with pre‐let‐7. Furthermore, the identification of the predicted most promising SMKI–miRNA interactions was validated by microscale thermophoresis, measuring direct binding affinities. This study evaluating the binding landscapes of the 78 FDA‐approved SMKIs with pre‐let‐7 miRNA served as an example highlighting the necessity to characterize the biological targets of SMKIs, many of which are FDA‐approved cancer agents, at the transcriptomic level with RNAs. The study also illustrates the possibility that the interaction with RNA targets may contribute to the observed biological and clinical performance of these approved SMKIs.

An integrated computational approach evaluating the binding between pre‐let‐7 microRNA and small‐molecule kinase inhibitors (SMKIs) revealed varied pre‐let‐7 binding affinities among the advanced SMKIs. The results justified the characterization of potential RNA targets for kinase inhibitors and small molecules with protein targets in general.© 2025 WILEY‐VCH GmbH

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