Binding of small organic molecules to macromolecular targets: evaluation of conformational entropy changes

The conformational entropy is the largest unfavorable effect that must be overcome during protein folding and binding. Accurate predictions of protein stability and binding affinity require a precise way of evaluating conformational entropy changes. Previously we implemented a computational approach aimed at estimating conformational entropy changes in peptides (D'Aquino et al., Proteins 1996;25:143-156; Lee et al., Proteins 1994;20:68-84). Here we extend this approach to estimate conformational entropy changes in molecules of pharmaceutical interest. Calculations were carried out for a set of 36 small organic molecules containing one dihedral angle and different functional groups around the central bond. Entropy changes were calculated for these molecules as the difference between the entropy of the free molecule and the entropy of the molecule when it is constrained to occupy a particular range of dihedrals, as in the bound state. Entropy changes for binding of larger molecules can be estimated assuming additivity on a per bond basis. Thus, the results presented here provide an initial toolbox of conformational entropy values in the form of a lookup table that can be used in the estimation of entropy changes associated with binding processes of more complex molecules. To facilitate their use, the values were parameterized in terms of the number and type of atoms neighboring each specific dihedral. Both methods, lookup table and parameterized equation, provide a very fast way of evaluating conformational entropy changes, making them suitable for fast screening algorithms.