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MARIO A. GARCÍA Y COLS. AN. R. ACAD. NAC. FARM.

FIGURE 2. Chemical structure of compound i52.

Superimposition

All the conformers resulting from the conformational search
were then superimposed to the ligand i52 (Figure 2) present in
the 1hov structure. This ligand was previously submitted to the
same conformational search analysis and followed the same
superimposition procedure in order to validate the methodology.
The criteria selected for the superimposition was the maximum
number of atoms fitted using the CSR program (25). Only the
conformers with the higher number of atoms fitted were selected for
the docking studies. The RMSD average of the selected ligands by
superimposition to i52 was 0.9345 ± 0.2543.

Docking

The docking studies were carried out using AutoDock 3.0 program
(26). Two different parameter sets for the zinc ion were used: the
implicit parameters for the zinc inside AutoDock program, and the
Stote and colleagues (27) which means r = 1.1 Å, e = 0.25 kcal/mol
and a formal charge of +2e. Very slight differences were observed
within both protocols (data not shown).

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