Discovery and Activity Verification of a O-GlcNAc Transferase Inhibitor by Structure-based Virtual Screening†

doi:10.7503/cjcu20170819

Abstract

Abstract:

A specific natural-product O-GleNAc transferase(OGT) inhibitor(Amentoflavone, AF) was identified from a structure-based virtual screening analysis. X-ray structure of the human OGT binding to uridine diphosphate(UDP) was used as the receptor in Discovery Studio 4.5. AF effectively inhibited OGT in a dose dependent and time dependent manner in vitro. The IC₅₀ value of this compound was 48.1 μmol/L. Western blot showed that O-GlcNAc modification of Nup62 by OGT in a cell free reaction system was decreased along with a shift in molecular weight by AF treatment. Furthermore, AF reduced global O-GlcNAcylation in a dose and time-dependent manner in Cos7 cells. Molecular dynamics analysis suggested that AF might form multiple hydrogens bonds with OGT in the same positions as the sugar donor UDP. This study validated the use of structure-based molecular docking to discover novel inhibitors of OGT. AF may be employed as a useful scaffold for the development of more potent OGT inhibitors in the future.

Key words: O-GlcNAc transferase, O-GlcNAc, Inhibitor, Virtual screening

CLC Number:

O626.32

TrendMD:

LIU Yubo, ZHANG Nana, CHEN Jinjiao, ZHU Tong, ZHANG Jianing, LI Wenli. Discovery and Activity Verification of a O-GlcNAc Transferase Inhibitor by Structure-based Virtual Screening^†[J]. Chem. J. Chinese Universities, 2018, 39(6): 1185.

Figures/Tables 7

Fig.1 Binding mode analysis of UDP-OGT

Fig.2 Identifcation of novel OGT inhibitors from a virtual screen(A) Eb distribution of the docking results about liginds, Lib-Dock(a) and C-Docker(b); (B) binding mode of ten hit compounds in human OGT by docking studies using Lib-Dock and C-Docker.

Table 1 Scoring results of virtual screening of candidate moleculars

No.	Compd.	Biological activity	E_b/(kJ·mol^-1)		Hydrogen bond
No.	Compd.	Biological activity	Lib-Dock	C-Docker	Hydrogen bond
1	Amentoflavone	Anti-inflammatory, anti-fungal	-146.7	-137.5	7
2	Robinin	Hydragogue	-130.5	-124.3	3
3	Griffipavixanthone	Cytotoxic	-127.5	-115.6	3
4	Dihydroxy-14-serraten-16-one	Cytotoxic	-126.3	-116.1	2
5	Daturametelin I	Anti-fungal, cytotoxic	-125.4	-114.3	2
6	Bisandrographolide A	Ion channelsagonist	-124.5	-113.9	2
7	Chloramultilide D	Anti-fungal, anti-inflammatory	-124.2	-111.4	2
8	Tetrahydroochnaflavone	Anti-fungal, anti-inflammatory	-123.1	-110.9	2
9	Pre-schisanartanin B	Cytotoxic	-122.9	-111.2	1
10	Isorhoifolin	Anti-fungal, anti-inflammatory, cytotoxic	-110.1	-109.2	1

Fig.3 In vitro activity of candidate compounds(A) Effect of candidates on OGT activities in a cell free reaction system, all the compounds were used at 50 μmol/L. ST045849 was used as a positive control. a. Amentoflavone; b. robinin; c. griffipavixanthone; d. dihydroxy-14-serraten-16-one; e. daturametelin I; f. bisandrographolide A; g. chloramultilide D; h. tetrahydroochnaflavone; i. pre-schisanartanin B; j. isorhoifolin; k. ST045849. (B) the chemical structure of AF.

Fig.4 Binding mode analysis of AF and OGT by MD(A) Binding pose of AF with OGT after MD; the residues of binding pocket were shown by surface; AF interacts with residues in the UDP-binding pocket of OGT; (B) binding mode analysis of UDP-OGT; (C) the root mean square fluctuation(RMSF) of OGT over 20 ns MD simulation.

Fig.5 AF inhibits OGT in vitro(A) AF inhibited OGT activity in a dose-dependent manner; (B) AF(50 μmol/L) inhibited O-GlcNAc modification of recombinant Nup62 in a cell-free reaction system.

Fig.6 AF inhibites OGT in cells(A) Western blots of Cos7 cell lysates after AF treatment at different doses(0—150 μmol/L) for 24 h; (B) western blots of Cos7 cell lysates after 50 μmol/L AF treatment for 6—24 h.

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