Structural Investigation of the Binding of 5‐Substituted Swainsonine Analogues to Golgi α‐Mannosidase II

Abstract

Golgi alpha-mannosidase II (GMII) is a key enzyme in the N-glycosylation pathway and is a potential target for cancer chemotherapy. The natural product swainsonine is a potent inhibitor of GMII. In this paper we characterize the binding of 5alpha-substituted swainsonine analogues to the soluble catalytic domain of Drosophila GMII by X-ray crystallography. These inhibitors enjoy an advantage over previously reported GMII inhibitors in that they did not significantly decrease the inhibitory potential of the swainsonine head-group. The phenyl groups of these analogues occupy a portion of the binding site not previously seen to be populated with either substrate analogues or other inhibitors and they form novel hydrophobic interactions. They displace a well-organized water cluster, but the presence of a C(10) carbonyl allows the reestablishment of important hydrogen bonds. Already approximately tenfold more active against the Golgi enzyme than the lysosomal enzyme, these inhibitors offer the potential of being extended into the N-acetylglucosamine binding site of GMII for the creation of even more potent and selective GMII inhibitors.

α-d-Mannose derivatives as models designed for selective inhibition of Golgi α-mannosidase II

“…4, a)] The identical binding pose of the aromatic chain was found for the docked 5-benzyl swainsonine at dGM (unpublished results). A similar binding position of an aromatic chain of nanomolar inhibitors close to Arg876 was recently described in the crystallographic measurements of 5-substituted aryl swainsonines with the dGM [4]. The interaction of 12 with tyrosine is missing in bLM because it is not conserved in known sequences of the lysosomal a-mannosidases [30].…”

“…This water has shown to be conserved in crystal structures of dGM either with intact substrates and inhibitors [4,5,21,22]. In all docking calculations the catalytic acid (Asp341 in dGM and Asp319 in bLM) was modeled in the protonated form in accordance with its catalytic role as a general acid.…”

“…Based on the above-mentioned results obtained from the evaluation of the alkyl sulfones 19 and 20 and crystallographic measurements of complexes of dGM with 5-substituted aryl derivatives of swainsonine selective inhibitors [4], the second set of the evaluated compounds (Scheme 2, Table 1) consisted of mannosides (thioglycosides 4 and 5, sulfoxides 8 and 9, sulfones 12 and 13) having aromatic aglycone connected to the sulfur atom through a short alkyl linker (one or two CH 2 groups). The main goal was to modify the aglycone unit of the glycosides to improve their selectivity toward GM.…”

“…The crystal structures of dGM with nanomolar inhibitor swainsonine (PDB ID: 3BLB) [4] and bLM (PDB ID: 1OD7) [30] were used as 3-D enzyme models of hGM and hLM for docking of synthesized mannosides by the GLIDE program [32,33] of the Schrödinger package [34].…”

“…Recently, the GlcNAc binding subsite at the active site of Drosophila melanogaster GM (dGM) was explored by crystallographic approach [21,22]. The regions of the active sites, at which selective inhibitors as well as moiety of the substrate responsible for the substrate specificity, were characterized based on crystal structures of dGM in combination with native substrate [21,22,29], swainsonine [20] and its 5-substituted derivatives [4].…”