Computer-aided design (CAD) of synzymes: Use of molecular mechanics (MM) for the rational design of superoxide dismutase mimics

Riley, Dennis P.,Henke, Susan L.,Lennon, Patrick J.,Aston, Karl

, p. 1908 - 1917 (2008/10/08)

Mn(II) complexes of C-substituted macrocyclic 1,4,7,10,13-pentaazacyclopentadecane ligands have been shown to be excellent functional mimics (Synzymes) of the native enzyme manganese Superoxide dismutase (Mn SOD). To better understand the profound effects that substituents exert on the SOD catalytic activity, we have utilized molecular mechanics (MM) calculations employing the CAChe system. Such a conformational analysis has made it possible to develop a consistent model that correlates catalytic rate with the ability of the ligand to adopt a folded geometry about the high-spin d5 spherically symmetrical Mn(II) ion, thus affording a six-coordinate pseudo-octahedral geometry (the geometry required by Mn(III)). This conformational analysis is consistent with the model that one of the nitrogen donors of the pentaaza crown ligand folds to occupy a pseudo-axial coordination position of an octahedron. The ΔE between the lowest energy folded ligand structure about Mn(II) and its corresponding Mn(III) structure correlates with catalytic activity; i.e., for a large series of complexes an excellent correlation is obtained for both the inner-sphere and outer-sphere rate constants for oxidation of Mn(II)-the rate-determining step in the catalytic cycle for these SOD mimics. From single-crystal X-ray structure determinations on several different members of this class of 7-coordinate dichloro(pentaaza crown) Mn(II) complexes, we have observed that the arrangement of NH's of the secondary amine donors is such that they alternate in their relative orientation to the plane generated by the five nitrogens and the Mn; i.e., the NH's are arranged in an up-down-up-down-up stereochemistry. Thus, one side of the plane of the macrocyclic ring possesses two nonadjacent NH's, while the opposite side has three NH's. Two unique folding motifs generated from MM calculations are found to correlate with the two pathways for Mn(II) oxidation: (1) the inner-sphere path correlates with an NH from the side of the two NH's folding into the axial octahedral coordination site, and (2) the outer-sphere path correlates with an NH from the side of the three NH's folded into an axial Oh site. MM calculations allow one to probe the effect that substituents on the macrocyclic ring carbons have on the relative energies of the Mn(II) and Mn(III) complexes with these ligands in the various potential folded geometries. The details of this modeling paradigm and the results of MM calculations utilizing the folding motif for a large number complexes are described. Of particular significance is the ability of the MM tool to predict correctly that certain substituent patterns and substituents enhance or reduce the contribution of one or the other pathway to the overall catalytic rate. The syntheses of several new complexes are reported and the rate constants for the two pathways of Mn(II) oxidation have been measured and found to correlate with the predictions arising from the energetics of folding as calculated by MM calculations.