DETERMINATION OF PHARMACOPHORIC GEOMETRY FOR COLLAGENASE INHIBITORS USING A NOVEL COMPUTATIONAL METHOD AND ITS VERIFICATION USING MOLECULAR-DYNAMICS, NMR, AND X-RAY CRYSTALLOGRAPHY

The pharmacophoric geometry for the inhibition of human fibroblast col lagenase has been determined using a novel computational method. The i nhibitors used in this study, which had from seven to 11 rotatable tor sion angles, did not show any irreversible movement from the pharmacop hore geometry during a 20 ps room temperature molecular dynamics simul ation. A parallel NMR study confirmed two torsion angles and a key ato m distance, and an X-ray crystallographic study of the protein-ligand complex established the model unequivocally. The X-ray structure showe d that nine out of 11 torsion angles were within the range predicted b y the pharmacophoric model. For one of the two remaining torsion angle s it suggested two possible values, one of which corresponded to the X -ray structure, Molecular dynamics simulations starting from the compu ted active conformation suggested that both of these two torsion angle s could have alternate values which included the X-ray value. The comp utational method described here is applicable to any general molecular superimposition problem which, in rational drug design, helps: (i) to visualize the similarities among the molecules of diverse structures; (ii) to determine the active conformation for inhibiting a certain bi ological system, which in turn can be used for developing SD-QSAR mode ls; and (iii) to dock new ligands at the active site of an enzyme or a biological receptor where the conformational correspondence with the X-ray crystallographically solved ligand is not obvious. The method us es multiple distance matrices to represent the conformational flexibil ity and conformational diversity. The molecules may be fairly flexible , with 10-12 rotatable torsion angles. No prior assumption of active c onformation is necessary during the fitting process; only a hypothesis of equivalent atoms is required to work with this method. The method suggests conformations which are within a predefined molecular mechani cs energy value and indicates the possibility of multiple conformation al solutions if the molecules are not sufficiently diverse or constrai ned.