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Protein-Ligand Dissociation Rate Constant from All-Atom Simulation.

Ekaterina Maximova1,2, Eugene B Postnikov3, Anastasia I Lavrova4,5

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Investigating isoniazid dissociation from catalase using accelerated molecular dynamics simulations, a novel extrapolation method yielded a dissociation time matching experimental values. This approach accurately predicts ligand-protein binding strength over vast timescales.

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Area of Science:

  • Biophysics
  • Computational Chemistry
  • Pharmacology

Background:

  • Understanding ligand-protein interactions is crucial for drug development.
  • Catalase is a vital enzyme, and its interaction with isoniazid, an antituberculosis drug, requires detailed investigation.
  • Accurate prediction of dissociation times is essential for characterizing drug efficacy and binding kinetics.

Purpose of the Study:

  • To investigate the dissociation of isoniazid from catalase using advanced simulation techniques.
  • To develop and validate a novel method for extrapolating dissociation times to zero-force conditions.
  • To compare simulation-derived dissociation times with experimental values.

Main Methods:

  • All-atom molecular dynamics (MD) simulations were employed.
  • Accelerated MD simulations, specifically τ-RAMD, were utilized to enhance ligand dissociation.
  • A new extrapolation approach based on a universal exponential force dependence was developed.

Main Results:

  • The study successfully calculated the dissociation time of isoniazid from catalase as 36.1 seconds.
  • The extrapolated value quantitatively matched the experimental dissociation time of 50 ± 8 seconds.
  • The novel extrapolation method proved effective over nine orders of magnitude in time.

Conclusions:

  • The developed τ-RAMD simulation and extrapolation methodology provides a reliable approach for predicting ligand-protein dissociation times.
  • This method offers a powerful tool for quantitatively assessing drug-target interactions.
  • The findings contribute to a deeper understanding of isoniazid's mechanism of action and binding kinetics with catalase.