Structural Determinants of Poly (ADP-Ribose) Polymerase Inhibition by Tetracyclines and Natural Compounds

Poly-Adenosine Diphosphate Ribose Polymerase (PARP) inhibitors induce DNA repair malfunction which result in cell death. PARP has two zinc finger domains, ZN1 and ZN2, which facilitate dimerization and binding to each end of broken DNA. This binding stabilizes the DNA strands and activates PARP. The Rossmann fold in PARP binds the cofactor NAD⁺. Extensive depletion of the NAD⁺ pool mediates PARP induced necrosis. PARP inhibitors have been particularly effective in the treatment of triple negative breast cancers (estrogen receptor, progesterone receptor and her2/neu negative) that contain BRCA mutations. PARP inhibitors target the catalytic NAD binding site. Using the PubChem database, over 200 natural compounds were collected with the nicotinamide pharmacophore. Our objective is to see if these compounds will directly bind to PARP by mimicking the nicotinamide binding mode and inhibit its activity. Quantitative data is generated and the ensemble of protein-ligand complexes were analyzed post rigid and flexible docking using SYBYL (Tripos, Inc). Ligands were rank ordered using a consensus scoring function which combines GOLD, DOCK, CHEM, CScore and PMF scoring functions. Top ligands retained interactions with NAD binding residues Gly-863 and Ser-904. Tetracyclines including the semi-synthetic antibiotic minocycline have higher binding affinity than known PARP inhibitor 3-Aminobenzamide. A high through-put colorimetric PARP assay is used to measure the incorporation of biotinylated poly(ADP-ribose) onto histone proteins. Preliminary results suggest that compounds with a carboxamide group attached to an aromatic ring are the better PARP inhibitors.