TY - JOUR

T1 - A New Class of Uracil-DNA Glycosylase Inhibitors Active against Human and Vaccinia Virus Enzyme

AU - Grin, Inga R.

AU - Mechetin, Grigory

AU - Kasymov, Rustem D.

AU - Diatlova, Evgeniia A.

AU - Yudkina, Anna

AU - Shchelkunov, Sergei N.

AU - Gileva, Irina P.

AU - Denisova, Alexandra A.

AU - Stepanov, Grigoriy A.

AU - Chilov, Ghermes G.

AU - Zharkov, Dmitry O.

N1 - Funding Information: Funding: This research was supported by the Russian Science Foundation (grant No. 17-14-01190 to I.R.G., biochemical and cell work). G.A.S. was funded within the framework of the Academic Fund Program at the HSE University in 2021 (grant No. 21-04-011). Partial salary support from the Russian Ministry of Science and Higher Education (State funded budget projects 0245-2021-0002 and FSUS-2020-0035 to D.O.Z.) is acknowledged. Publisher Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland.

PY - 2021/11/1

Y1 - 2021/11/1

N2 - Uracil–DNA glycosylases are enzymes that excise uracil bases appearing in DNA as a result of cytosine deamination or accidental dUMP incorporation from the dUTP pool. The activity of Family 1 uracil–DNA glycosylase (UNG) activity limits the efficiency of antimetabolite drugs and is essential for virulence in some bacterial and viral infections. Thus, UNG is regarded as a promising target for antitumor, antiviral, antibacterial, and antiprotozoal drugs. Most UNG inhibitors presently developed are based on the uracil base linked to various substituents, yet new pharmacophores are wanted to target a wide range of UNGs. We have conducted virtual screening of a 1,027,767-ligand library and biochemically screened the best hits for the inhibitory activity against human and vaccinia virus UNG enzymes. Although even the best inhibitors had IC50 ≥ 100 µM, they were highly enriched in a common fragment, tetrahydro-2,4,6-trioxopyrimidinylidene (PyO3). In silico, PyO3 preferably docked into the enzyme’s active site, and in kinetic experiments, the inhibition was better consistent with the competitive mechanism. The toxicity of two best inhibitors for human cells was independent of the presence of methotrexate, which is consistent with the hypothesis that dUMP in genomic DNA is less toxic for the cell than strand breaks arising from the massive removal of uracil. We conclude that PyO3 may be a novel pharmacophore with the potential for development into UNG-targeting agents.

AB - Uracil–DNA glycosylases are enzymes that excise uracil bases appearing in DNA as a result of cytosine deamination or accidental dUMP incorporation from the dUTP pool. The activity of Family 1 uracil–DNA glycosylase (UNG) activity limits the efficiency of antimetabolite drugs and is essential for virulence in some bacterial and viral infections. Thus, UNG is regarded as a promising target for antitumor, antiviral, antibacterial, and antiprotozoal drugs. Most UNG inhibitors presently developed are based on the uracil base linked to various substituents, yet new pharmacophores are wanted to target a wide range of UNGs. We have conducted virtual screening of a 1,027,767-ligand library and biochemically screened the best hits for the inhibitory activity against human and vaccinia virus UNG enzymes. Although even the best inhibitors had IC50 ≥ 100 µM, they were highly enriched in a common fragment, tetrahydro-2,4,6-trioxopyrimidinylidene (PyO3). In silico, PyO3 preferably docked into the enzyme’s active site, and in kinetic experiments, the inhibition was better consistent with the competitive mechanism. The toxicity of two best inhibitors for human cells was independent of the presence of methotrexate, which is consistent with the hypothesis that dUMP in genomic DNA is less toxic for the cell than strand breaks arising from the massive removal of uracil. We conclude that PyO3 may be a novel pharmacophore with the potential for development into UNG-targeting agents.

KW - DNA repair

KW - uracil-DNA glycosylase

KW - inhibitors

KW - virtual screening

KW - pyrimidines

KW - BASE EXCISION-REPAIR

KW - PROCESSIVITY FACTOR

KW - SELECTIVE-INHIBITION

KW - ESCHERICHIA-COLI

KW - VIRAL-DNA

KW - PROTEIN

KW - UNG

KW - REPLICATION

KW - STRATEGY

KW - SITE

KW - Uracil–DNA glycosylase

KW - Virtual screening

KW - Pyrimidines

KW - Inhibitors

KW - Humans

KW - Vaccinia virus/enzymology

KW - Enzyme Inhibitors/chemistry

KW - Molecular Structure

KW - Pyrimidines/chemistry

KW - Ligands

KW - Molecular Docking Simulation

KW - Kinetics

KW - Uracil-DNA Glycosidase/antagonists & inhibitors

UR - http://www.scopus.com/inward/record.url?scp=85119618403&partnerID=8YFLogxK

U2 - 10.3390/molecules26216668

DO - 10.3390/molecules26216668

M3 - Article

C2 - 34771075

VL - 26

JO - Molecules

JF - Molecules

SN - 1420-3049

IS - 21

M1 - 6668

ER -