Structural Basis of the Inhibition of Golgi α-Mannosidase II by Mannostatin A and the Role of the Thiomethyl Moiety in Ligand−Protein Interactions

The X-ray crystal structures of mannose trimming enzyme drosophila Golgi α-mannosidase II
(dGMII) complexed with the inhibitors mannostatin A (1) and an N-benzyl analogue (2) have been
determined. Molecular dynamics simulations and NMR studies have shown that the five-membered ring of
mannostatin A is rather flexible occupying pseudorotational itineraries between 2T3 and 5E, and 2T3 and 4E.
In the bound state, mannostatin A adopts a 2T1 twist envelope conformation, which is not significantly
populated in solution. Possible conformations of the mannosyl oxacarbenium ion and an enzyme-linked
intermediate have been compared to the conformation of mannostatin A in the cocrystal structure with
dGMII. It has been found that mannostatin A best mimics the covalent linked mannosyl intermediate, which
adopts a 1S5 skew boat conformation. The thiomethyl group, which is critical for high affinity, superimposes
with the C-6 hydroxyl of the covalent linked intermediate. This functionality is able to make a number of
additional polar and nonpolar interactions increasing the affinity for dGMII. Furthermore, the X-ray structures
show that the environment surrounding the thiomethyl group of 1 is remarkably similar to the arrangements
around the methionine residues in the protein. Collectively, our studies contradict the long held view that
potent inhibitors of glycosidases must mimic an oxacarbenium ion like transition state.