A novel small molecule inhibitor of the DNA repair protein Ku70/80

Eric - Weterings, Alfred C. Gallegos, Lauren N. Dominick, Laurence S. Cooke, Trace N. Bartels, Josef Vagner, Terry O Matsunaga, Daruka Mahadevan

Research output: Contribution to journalArticle

17 Citations (Scopus)

Abstract

Non-Homologous End-Joining (NHEJ) is the predominant pathway for the repair of DNA double strand breaks (DSBs) in human cells. The NHEJ pathway is frequently upregulated in several solid cancers as a compensatory mechanism for a separate DSB repair defect or for innate genomic instability, making this pathway a powerful target for synthetic lethality approaches. In addition, NHEJ reduces the efficacy of cancer treatment modalities which rely on the introduction of DSBs, like radiation therapy or genotoxic chemotherapy. Consequently, inhibition of the NHEJ pathway can modulate a radiation- or chemo-refractory disease presentation. The Ku70/80 heterodimer protein plays a pivotal role in the NHEJ process. It possesses a ring-shaped structure with high affinity for DSBs and serves as the first responder and central scaffold around which the rest of the repair complex is assembled. Because of this central position, the Ku70/80 dimer is a logical target for the disruption of the entire NHEJ pathway. Surprisingly, specific inhibitors of the Ku70/80 heterodimer are currently not available. We here describe an in silico, pocket-based drug discovery methodology utilizing the crystal structure of the Ku70/80 heterodimer. We identified a novel putative small molecule binding pocket and selected several potential inhibitors by computational screening. Subsequent biological screening resulted in the first identification of a compound with confirmed Ku-inhibitory activity in the low micro-molar range, capable of disrupting the binding of Ku70/80 to DNA substrates and impairing Ku-dependent activation of another NHEJ factor, the DNA-PKCS kinase. Importantly, this compound synergistically sensitized human cell lines to radiation treatment, indicating a clear potential to diminish DSB repair. The chemical scaffold we here describe can be utilized as a lead-generating platform for the design and development of a novel class of anti-cancer agents.

Original languageEnglish (US)
JournalDNA Repair
DOIs
StateAccepted/In press - Nov 17 2015

Fingerprint

Joining
DNA Repair
lysyl-arginyl-alanyl-lysyl-alanyl-lysyl-threonyl-threonyl-lysyl-lysyl-arginine
Repair
Molecules
DNA
Polynucleotide 5'-Hydroxyl-Kinase
Radiation
Neoplasms
Proteins
Double-Stranded DNA Breaks
Genomic Instability
Drug Discovery
Computer Simulation
Scaffolds
Radiotherapy
Screening
Drug Therapy
Cell Line
Cells

Keywords

  • Chemotherapy
  • DNA double strand break
  • Ku70/80
  • Non-Homologous End-Joining
  • Radiation
  • Small molecule inhibitor

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Cell Biology

Cite this

Weterings, E. ., Gallegos, A. C., Dominick, L. N., Cooke, L. S., Bartels, T. N., Vagner, J., ... Mahadevan, D. (Accepted/In press). A novel small molecule inhibitor of the DNA repair protein Ku70/80. DNA Repair. https://doi.org/10.1016/j.dnarep.2016.03.014

A novel small molecule inhibitor of the DNA repair protein Ku70/80. / Weterings, Eric -; Gallegos, Alfred C.; Dominick, Lauren N.; Cooke, Laurence S.; Bartels, Trace N.; Vagner, Josef; Matsunaga, Terry O; Mahadevan, Daruka.

In: DNA Repair, 17.11.2015.

Research output: Contribution to journalArticle

Weterings, Eric - ; Gallegos, Alfred C. ; Dominick, Lauren N. ; Cooke, Laurence S. ; Bartels, Trace N. ; Vagner, Josef ; Matsunaga, Terry O ; Mahadevan, Daruka. / A novel small molecule inhibitor of the DNA repair protein Ku70/80. In: DNA Repair. 2015.
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AU - Bartels, Trace N.

AU - Vagner, Josef

AU - Matsunaga, Terry O

AU - Mahadevan, Daruka

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AB - Non-Homologous End-Joining (NHEJ) is the predominant pathway for the repair of DNA double strand breaks (DSBs) in human cells. The NHEJ pathway is frequently upregulated in several solid cancers as a compensatory mechanism for a separate DSB repair defect or for innate genomic instability, making this pathway a powerful target for synthetic lethality approaches. In addition, NHEJ reduces the efficacy of cancer treatment modalities which rely on the introduction of DSBs, like radiation therapy or genotoxic chemotherapy. Consequently, inhibition of the NHEJ pathway can modulate a radiation- or chemo-refractory disease presentation. The Ku70/80 heterodimer protein plays a pivotal role in the NHEJ process. It possesses a ring-shaped structure with high affinity for DSBs and serves as the first responder and central scaffold around which the rest of the repair complex is assembled. Because of this central position, the Ku70/80 dimer is a logical target for the disruption of the entire NHEJ pathway. Surprisingly, specific inhibitors of the Ku70/80 heterodimer are currently not available. We here describe an in silico, pocket-based drug discovery methodology utilizing the crystal structure of the Ku70/80 heterodimer. We identified a novel putative small molecule binding pocket and selected several potential inhibitors by computational screening. Subsequent biological screening resulted in the first identification of a compound with confirmed Ku-inhibitory activity in the low micro-molar range, capable of disrupting the binding of Ku70/80 to DNA substrates and impairing Ku-dependent activation of another NHEJ factor, the DNA-PKCS kinase. Importantly, this compound synergistically sensitized human cell lines to radiation treatment, indicating a clear potential to diminish DSB repair. The chemical scaffold we here describe can be utilized as a lead-generating platform for the design and development of a novel class of anti-cancer agents.

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