An assay for DNA polymerase β lyase inhibitors that engage the catalytic nucleophile for binding

[Display omitted] DNA polymerase β (Pol β) repairs cellular DNA damage. When such damage is inflicted upon the DNA in tumor cells treated with DNA targeted antitumor agents, Pol β thus diminishes their efficacy. Accordingly, this enzyme has long been a target for antitumor therapy. Although numerous...

Full description

Saved in:
Bibliographic Details
Published in:Bioorganic & medicinal chemistry 2020-09, Vol.28 (17), p.115642-115642, Article 115642
Main Authors: Daskalova, Sasha M., Eisenhauer, Brian M., Gao, Mingxuan, Feng, Xizhi, Ji, Xun, Cheng, Qi, Fahmi, NourEddine, Khdour, Omar M., Chen, Shengxi, Hecht, Sidney M.
Format: Article
Language:English
Subjects:
Active site interaction
Enzyme modification
Lyase inhibitor
Non-proteinogenic amino acid
Targeted inhibitor selection
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:[Display omitted] DNA polymerase β (Pol β) repairs cellular DNA damage. When such damage is inflicted upon the DNA in tumor cells treated with DNA targeted antitumor agents, Pol β thus diminishes their efficacy. Accordingly, this enzyme has long been a target for antitumor therapy. Although numerous inhibitors of the lyase activity of the enzyme have been reported, none has yet proven adequate for development as a therapeutic agent. In the present study, we developed a new strategy to identify lyase inhibitors that critically engage the lyase active site primary nucleophile Lys72 as part of the binding interface. This involves a parallel evaluation of the effect of the inhibitors on the wild-type DNA polymerase β (Pol β) and Pol β modified with a lysine analogue at position 72. A model panel of five structurally diverse lyase inhibitors identified in our previous studies (only one of which has been published) with unknown modes of binding were used for testing, and one compound, cis-9,10-epoxyoctadecanoic acid, was found to have the desired characteristics. This finding was further corroborated by in silico docking, demonstrating that the predominant mode of binding of the inhibitor involves an important electrostatic interaction between the oxygen atom of the epoxy group and Nε of the main catalytic nucleophile, Lys72. The strategy, which is designed to identify compounds that engage certain structural elements of the target enzyme, could find broader application for identification of ligands with predetermined sites of binding.
ISSN:0968-0896
1464-3391
DOI:10.1016/j.bmc.2020.115642