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Prediction of Small-Molecule Partitioning into Biomolecular Condensates from Simulation.

Alina Emelianova1, Pablo L Garcia1, Daniel Tan1

  • 1Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States.

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Summary
This summary is machine-generated.

Understanding how small molecules enter biomolecular condensates is crucial for targeted drug development. This study reveals partitioning rules and develops predictive models (MAPPS) for condensate-specific therapeutics.

Keywords:
biomolecular condensatescoarse-grained modelmolecular dynamicspartitioningsmall molecules

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Area of Science:

  • Biophysics
  • Computational Chemistry
  • Drug Discovery

Background:

  • Predicting small-molecule partitioning into biomolecular condensates is vital for targeted drug development.
  • The molecular mechanisms governing this partitioning are not well understood.

Purpose of the Study:

  • To elucidate the physicochemical rules of small-molecule partitioning into condensates.
  • To develop efficient predictive models for small-molecule partitioning.
  • To explore condensate selectivity for therapeutic engineering.

Main Methods:

  • Atomistic molecular dynamics simulations of model condensates.
  • Development and application of minimal models for partitioning prediction (MAPPS).
  • Analysis of partitioning in condensates formed by FUS low-complexity domains (LCDs).

Main Results:

  • Hydrophobicity drives partitioning into hydrophobic condensates; specific interactions dominate polar condensates.
  • MAPPS accurately predicts partition coefficients in model and FUS LCD condensates.
  • Protein sequence influences small-molecule partitioning into condensates.

Conclusions:

  • Small-molecule partitioning depends on molecule-protein affinity and the interplay between compound properties and the condensate environment.
  • Condensate-specific therapeutics can be engineered based on these partitioning principles.
  • MAPPS provides an efficient tool for predicting small-molecule condensate partitioning.