Introduction of C-alkyl branches to l-iminosugars changes their active site binding orientation

Abstract

L-ido-Deoxynojirimycin (L-ido-DNJ) itself showed no affinity for human lysosomal acid α-glucosidase (GAA), whereas 5-C-methyl-L-ido-DNJ showed a strong affinity for GAA, comparable to the glucose analog DNJ, with a Ki value...

Design and Pharmacological Chaperone Effects of N-(4′-Phenylbutyl)-DAB Derivatives Targeting the Lipophilic Pocket of Lysosomal Acid α-Glucosidase

“…Focusing on the alkyl groups, we noticed that the N -alkyl groups of N -butyl-DAB ( 3f ) and N -(4′-phenylbutyl)-DAB ( 3c ) were accommodated in different pockets. We have previously reported the presence of three pockets of the ligand binding site in the study of 5- C -alkyl-L- ido -DNJ for GAA . It was observed that the alkyl chains of N -butyl-DAB ( 3f ) and N -(4′-phenylbutyl)-DAB ( 3c ) were accommodated in the different pockets in this study as well.…”

“…We have previously reported the presence of three pockets of the ligand binding site in the study of 5-C-alkyl-Lido-DNJ for GAA. 36 It was observed that the alkyl chains of N-butyl-DAB (3f) and N-(4′-phenylbutyl)-DAB (3c) were accommodated in the different pockets in this study as well. The alkyl chain of N-butyl-DAB (3f) was accommodated in the upper small pocket, while the alkyl chain of N-(4′phenylbutyl)-DAB (3c) was in the lower right pocket (Figure 3B,C).…”

“…Therefore, we prepared docking models of GAA with DAB, N -butyl-DAB ( 3f ), and N -(4′-phenylbutyl)-DAB ( 3c ) and attempted to elucidate the reason why the introduction of the N -butyl group into DAB reduced the affinity for GAA and the addition of the phenyl group to the N -butyl group increased that affinity using the docking analyses and the MD simulations. The docking analyses were performed according to a previously reported paper. , The three crystal structures of GAA complexed with DNJ, miglitol, and acarbose (PDB IDs: 5NN5, 5NN6, and 5NN8, respectively) were used as template structures in the docking analyses (Supporting Information, Figure S1). 36 docking grids were generated with all combinations of the water molecules nearby each ligand in the active site from GAA crystal structures using Glide’s Receptor Grid Generation module of Maestro.…”

“…The affinity of human lysosomal acid α-glucosidase (GAA) was performed according to our previous method. , Briefly, GAA activity was used in combination with Myozyme (Genzyme; Boston, MA) and 4-methylumbelliferyl-α- d -glucopyranoside (Sigma-Aldrich Co; St. Louis, Mo, USA). The reaction mixture consisted of 100 mM McIlvaine buffer (pH 5.2), 0.25% sodium taurocholate, 0.1% Triton X-100 (Nacalai Tesque Inc.; Kyoto, Japan), and an appropriate amount of enzyme.…”

“…In the present study, we first synthesized N -substituted derivatives of the enantiomeric DAB and LAB, respectively, and observed the changes in the inhibition spectra against the various glycosidases. Previous studies suggest that to achieve high affinity at the active site of GAA, it is effective not only to form appropriate amino acid interactions at the sugar recognition site but also to gain interaction at the lipophilic pocket by adding alkyl chains to the iminosugar. , This paper develops an original strategy for N -alkylated pyrrolidine iminosugars with high affinity to GAA that cross-link ligands for both the sugar recognition site and the lipophilic pocket. In the present study, we report optimization of the length of the N -alkyl chain as a spacer moiety and the substituents in the terminal benzene ring of N -(4′-phenylalkyl)-DAB and investigate their effect on the glycosidase inhibitions.…”