Journal of Chemical Biology

, Volume 8, Issue 3, pp 79–93 | Cite as

Design and activity of AP endonuclease-1 inhibitors

  • Zhiwei Feng
  • Stanton Kochanek
  • David Close
  • LiRong Wang
  • Ajay Srinivasan
  • Abdulrahman A. Almehizia
  • Prema Iyer
  • Xiang-Qun Xie
  • Paul A. Johnston
  • Barry Gold
Original Article
First Online:
Received:
Accepted:

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.

Keywords

AP endonuclease Abasic sites DNA repair Drug synergy Toxicity 

Abbreviations

AAG

Alkyladenine-DNA glycosylase (aka, MPG)

APE-1

Human apurinic endonuclease-1/redox effector factor-1

BER

Base excision repair

MD

Molecular dynamics

DMSO

Dimethyl sulfoxide

MeLex

Methyl 3-(1-methyl-5-(1-methyl-5-(propylcarbamoyl)-1H-pyrrol-3-ylcarbamoyl)-1H-pyrrol-3-ylamino)-3-oxopropane-1-sulfonate

RMSD

Root mean square deviation

Notes

Acknowledgements

Authors would like to acknowledge the funding support for the laboratory and Center at the University of Pittsburgh from NIH P30DA035778 (XIE), and the receipt of a Development Research Project award (Johnston and Gold) from the University of Pittsburgh Melanoma and Skin Cancer SPORE.

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

12154_2015_131_MOESM1_ESM.docx (849 kb)
ESM 1Synthetic Information and Structure Characterization of AJAY-4 (DOCX 848 kb)
12154_2015_131_MOESM2_ESM.docx (449 kb)
Table 1SStructural of compounds identified from in silico screen and Ki vs. APE-1 endonuclease activity. (DOCX 448 kb)
12154_2015_131_MOESM3_ESM.docx (3 mb)
Fig. 1SThe water-box for molecular dynamics (MD) simulations. The sizes were 62 × 62 × 62 Å3. The whole system (APE-1 and active compound AJAY-4,) contained ~6208 water molecules, 0 sodium ions and 4 chloride ions for a total of ~23071 atoms per periodic cell. MD simulations for 50 ns were performed. (DOCX 3038 kb)
12154_2015_131_MOESM4_ESM.docx (947 kb)
Fig. 2SInhibitors. (a) AJAY-1, IC50: 0.18uM, (b) AJAY-2, IC50: 0.22uM and (c) AJAY-3, IC50: 0.19 μM. His309 and Arg177 formed strong hydrogen bonds with all our four compounds. Tyr171, Asn174 and Asn212 formed weak hydrophilic interactions with these compounds. Phe266 formed strong π-π interaction with all compounds. Trp280 mainly formed hydrophobic interactions with our inhibitors. (DOCX 946 kb)
12154_2015_131_MOESM5_ESM.docx (440 kb)
Fig. 3SMD simulations results for inactive compound AJAY-15: (a) the alignments of AJAY-15 between before MD (orange) and after MD (blue), (b) the distances between AJAY-15 and APE-1. Although this compound matched with our five-point pharmacophore model, it showed no active for APE-1. Based our results, we found that inactive compound AJAY-15 did not form H-bonds with His309, and the distances between inactive compound AJAY-15, and Arg177 and His309 fluctuated significantly during the MS simulations. We suggest that Arg177 and His309 play key roles in the recognitions of inhibitors. (DOCX 439 kb)

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Copyright information

© Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

  1. 1.Department of Pharmaceutical SciencesUniversity of PittsburghPittsburghUSA
  2. 2.Malaria Vaccine Development ProgramNew DelhiIndia

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