Structure-based design of UDP-GlcNAc analogs as candidate GnT-V inhibitors

• Published in: Biochimica et biophysica acta. General subjects Vol. 1866; no. 6; p. 130118
• Main Authors: Vibhute, Amol M., Tanaka, Hide-nori, Mishra, Sushil K., Osuka, Reina F., Nagae, Masamichi, Yonekawa, Chizuko, Korekane, Hiroaki, Doerksen, Robert J., Ando, Hiromune, Kizuka, Yasuhiko
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.06.2022
• Subjects: cancer therapy; drugs; Glycobiology; Glycoproteins; Glycosylation; Glycosyltransferase; Humans; hydrophobicity; Inhibitor; N-acetylglucosaminyltransferase-V (GnT-V); N-glycan; neoplasm progression; Neoplasms; phosphates; Polysaccharides - chemistry; Polysaccharides - pharmacology; transferases; Uridine Diphosphate; KO; Glycosyltransferase; PHA; Glycosylation; GnT; Flu; PDB; PA; Glycobiology; PNS; N-acetylglucosaminyltransferase-V (GnT-V); Inhibitor; N-glycan; GlcNAc
• ISSN: 0304-4165; 1872-8006; 1872-8006
• DOI: 10.1016/j.bbagen.2022.130118

Background: N-Glycan branching regulates various functions of glycoproteins. N-Acetylglucosaminyltransferase V (GnT-V) is a GlcNAc transferase that acts on N-glycans and the GnT-V-producing branch is highly related to cancer progression. This indicates that specific GnT-V inhibitors may be drug candidates for cancer treatment. To design novel GnT-V inhibitors, we focused on the unique and weak recognition of the donor substrate UDP-GlcNAc by GnT-V. On the basis of the catalytic pocket structure, we hypothesized that UDP-GlcNAc analogs with increasing hydrophobicity may be GnT-V inhibitors. Methods: We chemically synthesized 10 UDP-GlcNAc analogs in which one or two phosphate groups were replaced with hydrophobic groups. To test these compounds, we set up an HPLC-based enzyme assay system for all N-glycan-branching GlcNAc transferases in which GnT-I–V activity was measured using purified truncated enzymes. Using this system, we assessed the inhibitory effects of the synthesized compounds on GnT-V and their specificity. Results: Several UDP-GlcNAc analogs inhibited GnT-V activity, although the inhibition potency was modest. Compared with other GnTs, these compounds showed a preference for GnT-V, which suggested that GnT-V was relatively tolerant of hydrophobicity in the donor substrate. Docking models of the inhibitory compounds with GnT-V suggested the mechanisms of how these compounds interacted with GnT-V and inhibited its action. Conclusions: Chemical modification of the donor substrate may be a promising strategy to develop selective inhibitors of GnT-V. General significance: Our findings provide new insights into the design of GnT inhibitors and how GnTs recognize the donor substrate. •GnT-V is a cancer-related glycosyltransferase forming a GlcNAc branch in N-glycans.•Recognition of the donor substrate UDP-GlcNAc by GnT-V is unique and weak.•Ten UDP-GlcNAc analogs were chemically synthesized as potential GnT-V inhibitors.•Some of these compounds inhibited GnT-V activity.