Protein Domain Specific Covalent Inhibition of Human DNA Polymerase β

• Published in: Chembiochem : a European journal of chemical biology 2021-08, Vol.22 (16), p.2619-2623
• Main Authors: Yuhas, Shelby C., Majumdar, Ananya, Greenberg, Marc M.
• Format: Article
• Language: English
• Subjects: Anisotropy; Base excision repair; Catalytic Domain; Communication; Communications; covalent inhibitors; Deoxyribonucleic acid; DNA; DNA - chemistry; DNA - metabolism; DNA damage; DNA polymerase; DNA Polymerase beta - antagonists & inhibitors; DNA Polymerase beta - chemistry; DNA Polymerase beta - metabolism; DNA polymerases; DNA repair; DNA-directed DNA polymerase; enzyme inhibition; Enzyme Inhibitors - chemistry; Enzyme Inhibitors - pharmacology; Fluorescence; Fluorescence Polarization; Humans; Inhibitors; Lysine; Protein Domains; Repair; Residues
• ISSN: 1439-4227; 1439-7633; 1439-7633
• DOI: 10.1002/cbic.202100247

DNA polymerase β (Pol β) is a frequently overexpressed and/or mutated bifunctional repair enzyme. Pol β possesses polymerase and lyase active sites, that are employed in two steps of base excision repair. Pol β is an attractive therapeutic target for which there is a need for inhibitors. Two mechanistically inspired covalent inhibitors (1, IC50=21.0 μM; 9, IC50=18.7 μM) that modify lysine residues in different Pol β active sites are characterized. Despite modifying lysine residues in different active sites, 1 and 9 inactivate the polymerase and lyase activities of Pol β. Fluorescence anisotropy experiments indicate that they do so by preventing DNA binding. Inhibitors 1 and 9 provide the basis for a general approach to preparing domain selective inhibitors of bifunctional polymerases. Such molecules could prove to be useful tools for studying the role of wild type and mutant forms of Pol β and other polymerases in DNA repair. A single synthesis and screening strategy yields covalent inhibitors that inactivate bifunctional DNA polymerase β by modifying lysine residues in different active site domains and prevent DNA binding.