1
|
Daskalova SM, Eisenhauer BM, Gao M, Feng X, Ji X, Cheng Q, Fahmi N, Khdour OM, Chen S, Hecht SM. An assay for DNA polymerase β lyase inhibitors that engage the catalytic nucleophile for binding. Bioorg Med Chem 2020; 28:115642. [PMID: 32773093 DOI: 10.1016/j.bmc.2020.115642] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/03/2020] [Accepted: 07/05/2020] [Indexed: 11/16/2022]
Abstract
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.
Collapse
Affiliation(s)
- Sasha M Daskalova
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States
| | - Brian M Eisenhauer
- Departments of Chemistry and Biology, University of Virginia, Charlottesville, VA 22904, United States
| | - Mingxuan Gao
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States
| | - Xizhi Feng
- Departments of Chemistry and Biology, University of Virginia, Charlottesville, VA 22904, United States
| | - Xun Ji
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States
| | - Qi Cheng
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States
| | - NourEddine Fahmi
- Departments of Chemistry and Biology, University of Virginia, Charlottesville, VA 22904, United States
| | - Omar M Khdour
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States
| | - Shengxi Chen
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States
| | - Sidney M Hecht
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States; Departments of Chemistry and Biology, University of Virginia, Charlottesville, VA 22904, United States
| |
Collapse
|