Protein–ligand binding free energies from exhaustive docking

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DOIResolve DOI: http://doi.org/10.1021/jp212646s
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TypeArticle
Journal titleThe Journal of Physical Chemistry B
Volume116
Issue23
Pages68726879; # of pages: 8
Subjectprotein-ligand binding; Monte Carlo and colecular dynamics simulations; elctrostatic models
AbstractWe explore the use of exhaustive docking as an alternative to Monte Carlo and molecular dynamics sampling for the direct integration of the partition function for protein–ligand binding. We enumerate feasible poses for the ligand and calculate the Boltzmann factor contribution of each pose to the partition function. From the partition function, the free energy, enthalpy, and entropy can be derived. All our calculations are done with a continuum solvation model that includes solving the Poisson equation. In contrast to Monte Carlo and molecular dynamics simulations, exhaustive docking avoids (within the limitations of a discrete sampling) the question of “Have we run long enough?” due to its deterministic complete enumeration of states. We tested the method on the T4 lysozyme L99A mutant, which has a nonpolar cavity that can accommodate a number of small molecules. We tested two electrostatic models. Model 1 used a solute dielectric of 2.25 for the complex apoprotein and free ligand and 78.5 for the solvent. Model 2 used a solute dielectric of 2.25 for the complex and apoprotein but 1.0 for the free ligand. For our test set of eight molecules, we obtain a reasonable correlation with a Pearson r2 = 0.66 using model 1. The trend in binding affinity ranking is generally preserved with a Kendall τ = 0.64 and Spearman ρ = 0.83. With model 2, the correlation is improved with a Pearson r2 = 0.83, Kendall τ = 0.93, and Spearman ρ = 0.98. This suggests that the energy function and sampling method adequately captured most of the thermodynamics of binding of the nonpolar ligands to T4 lysozyme L99A.
Publication date
PublisherACS Publications
LanguageEnglish
AffiliationNRC Biotechnology Research Institute; National Research Council Canada
Peer reviewedYes
NRC number53160
NPARC number21268210
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Record identifier92d20f58-ed85-460b-974d-eb2e4d929a1e
Record created2013-06-05
Record modified2017-03-23
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