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VOL. 73 (3), 703-746, 2007 ARE ADRENOMEDULLIN POSITIVE MODULATORS NOVEL...

bonds of the ligands were more than 10 (19). Trying to minimize
this difficulty, all compounds (1a to 3n) were submitted to a
conformational search using Macromodel in order to get the
maximum conformational diversity. The conformational search of all
compounds led to very similar conformers in terms of energy and, in
general, non-extended conformations as the most stable ones.

AutoDock was selected as the program to be used in the docking
procedures. The selection was based on its wide use in similar cases
described in the literature. In order to validate AutoDock as a docking
tool, the first ligand that followed this protocol (conformational
search, superimposition and docking) was compound i52 (32), the
ligand present in 1hov structure in the complex with MMP-2.
AutoDock was able to reproduce the NMR results and to predict the
conformation in which i52 is bound inside the MMP-2 active site.

Data Analysis

A perl-based program was developed to filter the vasta amount
of data generated. Distances and the angles between the ZBG, the
three catalytic histidines and the zinc ion, were calculated from
the docking results. Further analysis of the data allowed the
identification of the docked geometries with the adequate
coordination. For the MMP family, the pentacoordinated zinc has
been shown to be the most frequent coordination state (19), with
two possible geometries: trigonal bypiramide or square-based
pyramide. Both possibilities were scanned by the perl filter. The
analysis was set to a first limit of 2.53 Å of distance, and 0º of
variation from the angles described in the literature (28). The
distance of 2.53 Å is the maximum reported distance between a
coordinating atom and the Zn2+ reported for MMPs.

Following this protocol, 98 conformers were found to be able to
coordinate Zn ion inside any of the 11 NMR models. Table 4 shows
the ability of these compounds to bind the MMP-2 active site.
Complex MMP-2:i52 was submitted to the same perl filter leading to
only two positive hits. A detailed analysis of the 11 NMR complex
models, led to the observation that only models 1 and 3 fullfilled the
requiered distance and angle restrictions found in the literature for

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