Structural insights on the pamoic acid and the 8 kDa domain of DNA polymerase beta complex: Towards the design of higher-affinity inhibitors

We have performed docking studies of pamoic acid, a 9 micromolar pol beta inhibitor, and found that it binds in a single pocket at the surface of the 8 kDa domain of pol beta. However, docking studies provided five possible conformations for pamoic acid in this site. NMR experiments were performed on the complex to select a single conformation among the five retained. Chemical Shift Mapping data confirmed pamoic acid binding site found by docking while NOESY and saturation transfer experiments provided distances between pairs of protons from the pamoic acid and those of the 8 kDa domain that allowed the identification of the correct conformation.Combining NMR experiments on the complex with docking results allowed us to build a three-dimensional structural model. This model serves as the starting point for further structural studies aimed at improving the affinity of pamoic acid for binding to DNA polymerase beta.DNA polymerase β (pol beta) is the smallest human DNA polymerase and the first discovered adaptative polymerase. The structure of the full-length protein of 39 kDa has been solved by X ray cristallography [1]. It is divided into two structural subdomains, which have distinct functions. The first is termed the 8 kDa domain and is located at the N-terminal position. It binds to single-stranded and double stranded DNA, recognizes the 5'-phosphate group in gapped DNA and possesses dRP lyase activity [2]. The second, the C-terminal 31 kDa domain, displays the catalytic activity of polymerisation [3].Pol beta is the major enzyme of the single-stranded break DNA repair and base excision repair pathways [4-6]. It is able to remove damaged base residues, nucleotides and abasic sites arising from various endogenous and exogenous sources [7]. Thereby, when pol beta gene is deleted from mouse fibroblasts, hypersensitivity to monofunctional alkylation agents, e.g., methylmethanesulfonate, is observed [8,9]. Furthermore, pol beta is able to bypass DNA lesions which block