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Related Experiment Video

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High-throughput Screening for Chemical Modulators of Post-transcriptionally Regulated Genes
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Identification of Selective Small Molecule Modulators of mRNA Processing Using a Multiplexed QuantiGene

Sarah Sirin1, Nirodhini S Siriwardana1, Michael Wood1

  • 1Remix Therapeutics, Watertown, Massachusetts, USA.

Assay and Drug Development Technologies
|August 20, 2025
PubMed
Summary

Researchers developed a multiplexed assay for high-throughput screening (HTS) to find small molecules that modify mRNA processing. This method successfully identified selective modulators, advancing early drug discovery for mRNA targets.

Keywords:
HTScell-based screenhit callingmRNA processingmultiplexed HTSsmall molecule drug discovery

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Area of Science:

  • Molecular Biology
  • Drug Discovery
  • Assay Development

Background:

  • High-throughput screening (HTS) with multiplexed, cell-based assays is crucial for identifying modulators of biological processes.
  • Discovering small molecules that modulate mRNA processing requires sensitive and specific screening platforms.

Purpose of the Study:

  • To develop a multiplexed, bead-based HTS assay for quantifying multiple target gene transcripts simultaneously.
  • To identify selective small molecule modulators of mRNA processing using a novel QuantiGene assay on the Luminex platform.

Main Methods:

  • Developed a multiplexed, bead-based QuantiGene assay on the Luminex platform for simultaneous gene transcript quantification.
  • Implemented a dual-normalization hit-calling pipeline (plate- and well-based) to mitigate screening artifacts and plate variability.
  • Validated hits using an orthogonal, four-point concentration-response real-time PCR (qPCR) assay in a disease-relevant cell line.

Main Results:

  • The assay successfully identified unique compounds selectively modulating individual target genes involved in mRNA processing.
  • A dual-normalization strategy reduced false negatives and improved hit confirmation rates.
  • Chemical motif analysis revealed known and novel scaffolds enriched for specific targets, with only 5% of actives showing broad activity across three targets.

Conclusions:

  • The developed multiplexed HTS platform is a scalable and reliable strategy for identifying selective small molecule modulators of mRNA processing.
  • The assay demonstrates robustness and translational relevance, applicable to early drug discovery.
  • The findings highlight the platform's capacity for detecting highly selective modulators of complex biological pathways.