Targeting DNA Repair in Tumor Cells via Inhibition of ERCC1–XPF

Abstract

The ERCC1–XPF heterodimer is a 5′–3′ structure-specific endonuclease, which plays an essential role in several DNA repair pathways in mammalian cells. ERCC1–XPF is primarily involved in the repair of chemically induced helix-distorting and bulky DNA lesions, such as cyclobutane pyrimidine dimers (CPDs), and DNA interstrand cross-links. Inhibition of ERCC1–XPF has been shown to potentiate cytotoxicity of platinum-based drugs and cyclophosphamide in cancer cells. In this study, the previously described ERCC1–XPF inhibitor 4-((6-chloro-2-methoxyacridin-9-yl)­amino)-2-((4-methylpiperazin-1-yl)­methyl)­phenol (compound 1) was used as a reference compound. Following the outcome of docking-based virtual screening (VS), we synthesized seven novel derivatives of 1 that were identified in silico as being likely to have high binding affinity for the ERCC1–XPF heterodimerization interface by interacting with the XPF double helix–hairpin–helix (HhH2) domain. Two of the new compounds, 4-((6-chloro-2-methoxyacridin-9-yl)­amino)-2-((4-cyclohexylpiperazin-1-yl)­methyl)­phenol (compound 3) and 4-((6-chloro-2-methoxyacridin-9-yl)­amino)-2-((4-(2-(dimethylamino)­ethyl) piperazin-1-yl) methyl) phenol (compound 4), were shown to be potent inhibitors of ERCC1–XPF activity in vitro. Compound 4 showed significant inhibition of the removal of CPDs in UV-irradiated cells and the capacity to sensitize colorectal cancer cells to UV radiation and cyclophosphamide.

Computer‐aided drug design of small molecule inhibitors of the ERCC1‐XPF protein–protein interaction

“…Using classical MD simulations, we compared the unbound, F06‐bound, and ERCC1‐bound form of the HhH2 domain of XPF (residues 822–905). For the F06‐XPF complex, we used the structure previously obtained from docking simulations (Elmenoufy et al, ). The unbound and ERCC1‐bound forms were extracted from the NMR ensemble of ERCC1‐XPF dimerized HhH2 domains (PDB 1Z00) (Tripsianes et al, ), where the bound ERCC1 structure was excluded and included in the simulation, respectively.…”

“…Using the MOE (Molecular Operating Environment) Pharmacophore Query Editor and the EHT scheme, we generated a set of essential pharmacophore features of F06, based on the docking pose of the compound (Lin, ). Electrostatic maps of the binding site were generated as reported previously (Elmenoufy et al, ).…”

“…In order to rank the analogues generated in the previous step, we adopted the same structure‐based virtual screening (VS) strategy that we successfully used before (Elmenoufy et al, ). Molecular docking simulations were run with MOE Dock (Chemical Computing Group Inc ).…”

“…More recently, we successfully combined computer‐aided drug design (CADD) with a structure–activity relationship approach to extend the piperazine ring of F06 with different substituents, in order to improve the biological activity of this class of compounds. In this way, we assessed F06 as a suitable scaffold for developing DNA repair inhibitor drug candidates (Elmenoufy et al, ). Building on our previous results, we report a new CADD strategy for further improvement of F06, which uses molecular dynamics (MD) to characterize in detail the structural changes introduced by F06 binding to XPF compared to XPF free form and ERCC1‐XPF heterodimer.…”

“…We also evaluated the hydrogen bond network of F06 with XPF in order to design F06 analogues with enhanced protein interaction patterns. In contrast to our earlier study where we modified a solvent‐exposed group of F06 (Elmenoufy et al, ), here we focused on different modifications such as truncation of the lateral branch of F06 and substitution of the methoxy group with hydrogen bond acceptor groups to improve buried ligand–receptor interactions. Through our CADD‐driven medicinal chemistry strategy, we developed B5 , an analogue showing 3‐fold increased inhibition of the ERCC1‐XPF incision activity in vitro.…”