Challenges Encountered Applying Equilibrium and Nonequilibrium Binding Free Energy Calculations

Abstract

Binding free energy calculations have become increasingly valuable to drive decision making in drug discovery projects. However, among other issues, inadequate sampling can reduce accuracy, limiting the value of the technique.In this paper we apply absolute binding free energy calculations to ligands binding to T4 lysozyme L99A and HSP90 using equilibrium and non-equilibrium approaches. We highlight sampling problems encountered in these systems, such as slow side chain rearrangements and slow changes of water placement upon ligand binding. These same types of challenges are likely to show up in other protein-ligand systems as well and we propose some strategies to diagnose and test for such problems in alchemical free energy calculations. We also explore similarities and differences in how the equilibrium and the non-equilibrium approaches handle these problems. Our results show the large amount of work still to be done to make free energy calculations robust and reliable and provide insight for future research in this area. File list (2)download file view on ChemRxiv NEQ_binding.pdf (30.14 MiB) download file view on ChemRxiv SI.pdf (8.25 MiB)

Alchemical absolute protein–ligand binding free energies for drug design

“…It has been observed that relying on the statistical uncertainties from the ∆G estimators, either analytical expressions, or bootstrapped values, may not be reliable. 5,38 Therefore, in this work we rely on independent repeats of the whole free energy calculation procedure to gain access to the variation of the ∆G estimates. 14,46 Subsequently, we incorpo-rate both, uncertainties from the independent replicas and statistical uncertainty from the estimator by means of bootstrap into a single uncertainty value.…”

“…This allows one to explicitly include the different apo and holo end-states into the same calculation 17 . Several recent applications of the NEQ approach on model host-guest systems showed promising results for the calculation of absolute binding free energies 5,27,37 .…”

“… 17 Several recent applications of the NEQ approach on model host–guest systems showed promising results for the calculation of absolute binding free energies. 5,27,37 …”

Alchemical Absolute Protein-Ligand Binding Free Energies for Drug Design

“…It has been observed that relying on the statistical uncertainties from the ∆G estimators, either analytical expressions, or bootstrapped values, may not be reliable. 4,35 Therefore, in this work we rely on independent repeats of the whole free energy calculation procedure to gain access to the variation of the ∆G estimates. 13,42 Subsequently, we incorporate both, uncertainties from the independent replicas and statistical uncertainty from the estimator by means of bootstrap into a single uncertainty value.…”

“…This allows one to explicitly include the different apo and holo end-states into the same calculation 16 . Several recent applications of the NEQ approach on model host-guest systems showed promising results for the calculation of absolute binding free energies 4,25,34 .…”