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TIES 20: Relative Binding Free Energy with a Flexible Superimposition Algorithm and Partial Ring Morphing.

Mateusz K Bieniek1, Agastya P Bhati1, Shunzhou Wan1

  • 1Centre for Computational Science, Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom.

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Summary
This summary is machine-generated.

The enhanced Thermodynamic Integration with Enhanced Sampling (TIES) protocol, using a new superimposition algorithm and partial ring morphing, accurately predicts relative binding free energies. This computational chemistry method improves precision for drug discovery applications.

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Area of Science:

  • Computational Chemistry
  • Molecular Modeling
  • Drug Discovery

Background:

  • Accurate calculation of relative binding free energies is crucial for drug discovery.
  • The Thermodynamic Integration with Enhanced Sampling (TIES) protocol is a key computational method.
  • Ligand atom matching is essential for TIES protocol validity.

Purpose of the Study:

  • To implement and validate a flexible topology superimposition algorithm for TIES.
  • To enable matching and morphing of partial rings within the TIES protocol.
  • To improve the precision of predicted relative binding free energies.

Main Methods:

  • Developed an exhaustive joint-traversal algorithm for largest common component identification.
  • Applied the algorithm to enable partial ring matching and morphing in TIES.
  • Validated the improved TIES protocol using 55 transformations across five proteins.

Main Results:

  • TIES 20 with RESP charges and the new algorithm achieved a mean unsigned error of 0.75 kcal/mol.
  • Enabling partial ring morphing significantly improved prediction precision.
  • AM1-BCC charge system further improved agreement with experimental data by over 10%.

Conclusions:

  • The enhanced TIES protocol with ring morphing offers improved precision in free energy predictions.
  • Ensemble simulations are critical due to the non-normal distribution of free energy data.
  • The new superimposition algorithm enhances the reliability of TIES for computational chemistry applications.