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Improving Sampling of Binding Free Energy Differences between Covalently Bound Ligands in Alternate Binding Pockets
Anika J Friedman1, Jerome M Fox1, Michael R Shirts1
1Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado80309, United States.
Journal of Chemical Theory and Computation
|August 11, 2026
Summary
Achieving accurate molecular simulations for complex systems is challenging due to sampling limitations. A new method, multiple topology replica exchange of expanded ensemble (MT-REXEE), enhances sampling for flexible binding complexes with high free energy barriers.
Area of Science:
- Computational Chemistry
- Molecular Dynamics
- Biophysics
Background:
- Alchemical free energy methods are crucial for molecular simulations but limited by sampling efficiency.
- Complex molecular systems, such as flexible binding complexes, present significant sampling challenges due to high free energy barriers.
- Accurate free energy estimates require sufficient uncorrelated samples, often difficult to obtain with standard simulation techniques.
Purpose of the Study:
- To develop and evaluate an enhanced sampling approach for improving the efficiency of molecular simulations in complex systems.
- To address the limitations in sampling associated with flexible binding complexes and high free energy barriers.
- To demonstrate the utility of the new method for unbiased sampling of alternate configurational states without prior pocket definitions.
Main Methods:
- The study employed the multiple topology replica exchange of expanded ensemble (MT-REXEE) enhanced sampling approach.
- MT-REXEE adaptively grows and shrinks molecular chains within the simulation ensemble to facilitate transitions between different binding states.
- This method was applied to the complex formed between FabB and acyl carrier protein (ACP) in Escherichia coli, and also tested on mouse major urinary protein 1 ligands.
Main Results:
- MT-REXEE achieved highly efficient sampling of multiple binding pockets in the FabB-ACP complex.
- The approach enabled unbiased sampling of alternate configurational states for large, complex systems.
- Faster convergence of free energy estimates was observed for small molecule binding, demonstrating enhanced sampling capabilities.
Conclusions:
- MT-REXEE is a valuable addition to enhanced sampling methods, particularly for systems with high free energy barriers.
- The method provides a powerful tool for unbiased sampling of complex molecular systems, including those with flexible binding partners.
- An open-source implementation of MT-REXEE is available, facilitating its application in computational chemistry and drug discovery.
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