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VOL. 76 (2), 223-239, 2010 PREDICTION OF LIGAND BINDING ENERGY...

where R is the gas constant, T is temperature (Kelvin) and Kd is
the dissociation constant. The calculated ?Gbind values were obtained
by the LIE approximation using the energy contributions retrieved
from MD trajectories of free and bound ligand and were used in a
linear regression test to determinate if they are statistically related
with the experimental ?Gbind using the GNU/PSPP 0.6.1 program (13).

The use of PME (Particle-Mesh-Ewald) dealing with the long
range electrostatic interactions was specially considered as in LIE
method only short-range contributions are taking into account. The
results of the test yield in a very low energy contribution of the PME
to the total electrostatic energy so all effects of periodic boundary
conditions and PME can be neglected for the low size of the system.

3. RESULTS

3.1. Docking

In a first approach, dexamethasone was evaluated in a docking
assay to determine if the protocol was able to predict the
crystallographic position with an acceptable value of RMSD and to
validate the method for further evaluation of flavonoids. The docked
conformation with the best energy was found with a RMSD value
less than 1.0 amstrong, so the method was confirmed to be capable
of found the correct conformation. Identical experiments were
carried out with the rest of ligands in the training set (betamethasone
and cortisol) and similar results were obtained, and therefore a
binding mode for molecule in training set was identified.

Once the method was validated, we applied it to the compounds of
the test set (Table 1). The results of these experiments were evaluated
and were used to identify potential interactions with the GR. Mainly
two kinds of interactions were found in the training and test sets:
Hydrogen bonds and hydrophobic interactions. The first kind is due
to the interactions that occur between the hydroxyl and ketone groups
of the ligands and polar residues surrounding the cavity that binds the
ligand. The second kind occurs when aromatic rings of the ligands
interact with highly apolar residues around the cavity.

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