title: Design and activity of AP endonuclease-1 inhibitors.
abstract: Apurinic/apyrimidinic endonuclease-1/redox effector factor-1 (APE-1) is a critical component of base excision repair that excises abasic lesions created enzymatically by the action of DNA glycosylases on modified bases and non-enzymatically by hydrolytic depurination/depyrimidination of nucleobases. Many anticancer drugs generate DNA adducts that are processed by base excision repair, and tumor resistance is frequently associated with enhanced APE-1 expression. Accordingly, APE-1 is a potential therapeutic target to treat cancer. Using computational approaches and the high resolution structure of APE-1, we developed a 5-point pharmacophore model for APE-1 small molecule inhibitors. One of the nM APE-1 inhibitors (AJAY-4) that was identified based on this model exhibited an overall median growth inhibition (GI50) of 4.19 μM in the NCI-60 cell line panel. The mechanism of action is shown to be related to the buildup of abasic sites that cause PARP activation and PARP cleavage, and the activation of caspase-3 and caspase-7, which is consistent with cell death by apoptosis. In a drug combination growth inhibition screen conducted in 10 randomly selected NCI-60 cell lines and with 20 clinically used non-genotoxic anticancer drugs, a synergy was flagged in the SK-MEL-5 melanoma cell line exposed to combinations of vemurafenib, which targets melanoma cells with V600E mutated BRAF, and AJAY-4, our most potent APE-1 inhibitor. The synergy between AJAY-4 and vemurafenib was not observed in cell lines expressing wild-type B-Raf protein. This synergistic combination may provide a solution to the resistance that develops in tumors treated with B-Raf-targeting drugs.
authors.affiliation: Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261 USA.
authors.forename: Zhiwei
authors.initials: Z
authors.lastname: Feng
authors.affiliation: Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261 USA.
authors.forename: Stanton
authors.initials: S
authors.lastname: Kochanek
authors.affiliation: Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261 USA.
authors.forename: David
authors.initials: D
authors.lastname: Close
authors.affiliation: Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261 USA.
authors.forename: LiRong
authors.initials: L
authors.lastname: Wang
authors.affiliation: Malaria Vaccine Development Program, New Delhi, 110067 India.
authors.forename: Ajay
authors.initials: A
authors.lastname: Srinivasan
authors.affiliation: Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261 USA.
authors.forename: Abdulrahman A
authors.initials: AA
authors.lastname: Almehizia
authors.affiliation: Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261 USA.
authors.forename: Prema
authors.initials: P
authors.lastname: Iyer
authors.affiliation: Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261 USA.
authors.forename: Xiang-Qun
authors.initials: XQ
authors.lastname: Xie
authors.affiliation: Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261 USA.
authors.forename: Paul A
authors.initials: PA
authors.lastname: Johnston
authors.affiliation: Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261 USA.
authors.forename: Barry
authors.identifier: 0000-0002-2610-978X
authors.initials: B
authors.lastname: Gold
keywords: AP endonuclease; Abasic sites; DNA repair; Drug synergy; Toxicity