A Three-Dimensional Quantitative Structure-Activity Relationship Study of the Inhibition of the ATPase Activity and the Strand Passing Catalytic Activity of Topoisomerase IIα by Substituted Purine Analogs

Based on the topoisomerase IIα catalytic inhibitory activity of a previous hit compound, NSC35866, we screened 40 substituted purines or purine-like compounds from the National Cancer Institute repository for their ability to inhibit the ATPase activity of human topoisomerase IIα. Several compounds, including NSC348400, NSC348401 and NSC348402, were inhibitory at submicromolar concentrations. Three-dimensional quantitative structure-activity relationship models using comparative molecular field and comparative molecular similarity indices analyses were constructed using 24 of these compounds. The ability of 10 selected compounds to inhibit the complete DNA strand passage reaction of topoisomerase IIα correlated well with their potency as ATPase inhibitors. None of the 40 compounds significantly increased levels of the topoisomerase IIα-DNA covalent complex, suggesting that they functioned as catalytic topoisomerase II inhibitors and not as topoisomerase II poisons. Although some of these compounds could antagonize the effect of etoposide on the level of topoisomerase IIα-DNA covalent complex formation in vitro, in contrast to NSC35866, they were not capable of antagonizing etoposide-induced cytotoxicity and DNA strand breaks in cells. Two independently selected human SCLC cell lines with reduced topoisomerase IIα expression displayed cross-resistance to NSC348400, NBSC348401, and NSC348402, whereas an MDR1 line was fully sensitive. These results suggest that topoisomerase IIα is a functional cellular target for most of these substituted purine compounds and that these compounds do not display MDR1 liability.

[1]  S. Rault,et al.  Comparative molecular field analysis of CCK-B antagonists , 1994 .

[2]  M. Sehested,et al.  Combining Etoposide and Dexrazoxane Synergizes with Radiotherapy and Improves Survival in Mice with Central Nervous System Tumors , 2005, Clinical Cancer Research.

[3]  M. Sehested,et al.  Antagonistic effect of the cardioprotector (+)-1,2-bis(3,5-dioxopiperazinyl-1-yl)propane (ICRF-187) on DNA breaks and cytotoxicity induced by the topoisomerase II directed drugs daunorubicin and etoposide (VP-16). , 1993, Biochemical pharmacology.

[4]  K. Kohn,et al.  Alkaline elution analysis, a new approach to the study of DNA single-strand interruptions in cells. , 1973, Cancer research.

[5]  D. Scudiero,et al.  Substituted purine analogues define a novel structural class of catalytic topoisomerase II inhibitors. , 2005, Cancer research.

[6]  JAMES C. Wang,et al.  Cellular roles of DNA topoisomerases: a molecular perspective , 2002, Nature Reviews Molecular Cell Biology.

[7]  L. Liu,et al.  A model for tumor cell killing by topoisomerase poisons. , 1990, Cancer cells.

[8]  J. Lindsley,et al.  Steady-state and Rapid Kinetic Analysis of Topoisomerase II Trapped as the Closed-clamp Intermediate by ICRF-193* , 2000, The Journal of Biological Chemistry.

[9]  Frank S. Guziec,et al.  Structure-activity study of the interaction of bioreductive benzoquinone alkylating agents with DNA topoisomerase II , 2005, Cancer Chemotherapy and Pharmacology.

[10]  N. Osheroff,et al.  Stabilization of eukaryotic topoisomerase II-DNA cleavage complexes. , 2003, Current topics in medicinal chemistry.

[11]  D. Botstein,et al.  DNA topoisomerase II is required at the time of mitosis in yeast , 1985, Cell.

[12]  R. Cramer,et al.  Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins. , 1988, Journal of the American Chemical Society.

[13]  M. Sehested,et al.  DNA topoisomerase II rescue by catalytic inhibitors: a new strategy to improve the antitumor selectivity of etoposide. , 1997, Biochemical pharmacology.

[14]  N. Zhou,et al.  DNA Damage-mediated Apoptosis Induced by Selenium Compounds* , 2003, Journal of Biological Chemistry.

[15]  M. Sehested,et al.  Maleimide is a potent inhibitor of topoisomerase II in vitro and in vivo: a new mode of catalytic inhibition. , 2002, Molecular pharmacology.

[16]  N. Osheroff,et al.  Cobalt enhances DNA cleavage mediated by human topoisomerase II alpha in vitro and in cultured cells. , 2004, Biochemistry.

[17]  M. Sehested,et al.  Human small cell lung cancer NYH cells resistant to the bisdioxopiperazine ICRF‐187 exhibit a functional dominant Tyr165Ser mutation in the Walker A ATP binding site of topoisomerase IIα , 2002, FEBS letters.

[18]  M. Sehested,et al.  Mapping of DNA topoisomerase II poisons (etoposide, clerocidin) and catalytic inhibitors (aclarubicin, ICRF-187) to four distinct steps in the topoisomerase II catalytic cycle. , 1996, Biochemical pharmacology.

[19]  Wei Li,et al.  DNA topoisomerase IIβ and neural development , 2000 .

[20]  J. Lindsley Use of a real-time, coupled assay to measure the ATPase activity of DNA topoisomerase II. , 2001, Methods in molecular biology.

[21]  W. Ens,et al.  Biochemical and Proteomics Approaches to Characterize Topoisomerase IIα Cysteines and DNA as Targets Responsible for Cisplatin-Induced Inhibition of Topoisomerase IIα , 2005, Molecular Pharmacology.

[22]  N. Akimitsu,et al.  Enforced cytokinesis without complete nuclear division in embryonic cells depleting the activity of DNA topoisomerase IIα , 2003, Genes to cells : devoted to molecular & cellular mechanisms.

[23]  H. Koyama,et al.  Hypersensitivity of Nonhomologous DNA End-joining Mutants to VP-16 and ICRF-193 , 2003, Journal of Biological Chemistry.

[24]  M. Sehested,et al.  Improved targeting of brain tumors using dexrazoxane rescue of topoisomerase II combined with supralethal doses of etoposide and teniposide. , 1998, Clinical cancer research : an official journal of the American Association for Cancer Research.

[25]  D. Eastmond,et al.  Catalytic inhibitors of topoisomerase II are DNA‐damaging agents: induction of chromosomal damage by merbarone and ICRF‐187 , 2002, Environmental and molecular mutagenesis.

[26]  H. Koyama,et al.  Decreased topoisomerase IIα expression confers increased resistance to ICRF-193 as well as VP-16 in mouse embryonic stem cells , 2001 .

[27]  L. Liu,et al.  Stimulation of topoisomerase II-mediated DNA damage via a mechanism involving protein thiolation. , 2001, Biochemistry.

[28]  J. Berger,et al.  Structure of the topoisomerase II ATPase region and its mechanism of inhibition by the chemotherapeutic agent ICRF-187 , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[29]  G. Klebe,et al.  Molecular similarity indices in a comparative analysis (CoMSIA) of drug molecules to correlate and predict their biological activity. , 1994, Journal of medicinal chemistry.

[30]  A. Escargueil,et al.  Catalytic topoisomerase II inhibitors in cancer therapy. , 2003, Pharmacology & therapeutics.

[31]  T. Andoh,et al.  Catalytic inhibitors of DNA topoisomerase II. , 1998, Biochimica et biophysica acta.

[32]  H. Hansen,et al.  Differential cytotoxicity of 19 anticancer agents in wild type and etoposide resistant small cell lung cancer cell lines. , 1993, British Journal of Cancer.

[33]  H. Kubinyi,et al.  Three-dimensional quantitative similarity-activity relationships (3D QSiAR) from SEAL similarity matrices. , 1998, Journal of medicinal chemistry.