6VBA

Structure of human Uracil DNA Glycosylase (UDG) bound to Aurintricarboxylic acid (ATA)

Summary for 6VBA

• Entry DOI: 10.2210/pdb6vba/pdb
• Related: 1AKZ
• Descriptor: Uracil-DNA glycosylase, 3,3'-[(3-carboxy-4-oxocyclohexa-2,5-dien-1-ylidene)methylene]bis(6-hydroxybenzoic acid) (3 entities in total)
• Functional Keywords: glycosylase, dna repair, uracil removal from dna, alpha/ beta protein, glycosidase, hydrolase
• Biological source: Homo sapiens (Human)
• Total number of polymer chains: 1
• Total formula weight: 25966.48

Authors

Moiani, D.,Arvai, A.S.,Tainer, J.A. (deposition date: 2019-12-18, release date: 2021-03-03, Last modification date: 2023-10-11)

Primary citation

Nguyen, M.T.,Moiani, D.,Ahmed, Z.,Arvai, A.S.,Namjoshi, S.,Shin, D.S.,Fedorov, Y.,Selvik, E.J.,Jones, D.E.,Pink, J.,Yan, Y.,Laverty, D.J.,Nagel, Z.D.,Tainer, J.A.,Gerson, S.L.
An effective human uracil-DNA glycosylase inhibitor targets the open pre-catalytic active site conformation.
Prog.Biophys.Mol.Biol., 163:143-159, 2021

PubMed Abstract: Human uracil DNA-glycosylase (UDG) is the prototypic and first identified DNA glycosylase with a vital role in removing deaminated cytosine and incorporated uracil and 5-fluorouracil (5-FU) from DNA. UDG depletion sensitizes cells to high APOBEC3B deaminase and to pemetrexed (PEM) and floxuridine (5-FdU), which are toxic to tumor cells through incorporation of uracil and 5-FU into DNA. To identify small-molecule UDG inhibitors for pre-clinical evaluation, we optimized biochemical screening of a selected diversity collection of >3,000 small-molecules. We found aurintricarboxylic acid (ATA) as an inhibitor of purified UDG at an initial calculated IC < 100 nM. Subsequent enzymatic assays confirmed effective ATA inhibition but with an IC of 700 nM and showed direct binding to the human UDG with a K of <700 nM. ATA displays preferential, dose-dependent binding to purified human UDG compared to human 8-oxoguanine DNA glycosylase. ATA did not bind uracil-containing DNA at these concentrations. Yet, combined crystal structure and in silico docking results unveil ATA interactions with the DNA binding channel and uracil-binding pocket in an open, destabilized UDG conformation. Biologically relevant ATA inhibition of UDG was measured in cell lysates from human DLD1 colon cancer cells and in MCF-7 breast cancer cells using a host cell reactivation assay. Collective findings provide proof-of-principle for development of an ATA-based chemotype and "door stopper" strategy targeting inhibitor binding to a destabilized, open pre-catalytic glycosylase conformation that prevents active site closing for functional DNA binding and nucleotide flipping needed to excise altered bases in DNA.

PubMed: 33675849
DOI: 10.1016/j.pbiomolbio.2021.02.004

Experimental method

X-RAY DIFFRACTION (1.8 Å)