Effect of ATR and Chk1 inhibition on processing of stalled replication forks at the psoralen ICL.

<p>(A) pTUC-PSO was incubated for 95 min in a Xenopus egg extract in absence (NT; not treated) or presence of 5 mM caffeine or 10 µM UCN-01 and [α-³²P]-dATP and analyzed on 2D gels. Total signal and spots 1, 2 and 3 (as labeled on the interpretative diagram) were quantified in the presence of caffeine (B), UCN-01 (C), KU55933 (D) or C3742 (E). Results were normalized to the signals obtained with the non-treated plasmid. Exp1, Exp2, Exp3, Exp4, Exp5 and Exp6 are six experiments in six independently prepared egg extracts.</p

Replication fork leading strands progress up to the psoralen crosslink.

<p>(A) Sequence of the plasmid around the psoralen ICL with restriction sites used in B and C. Double arrows indicate the size of the replicated strands (lagging or leading) spanning the ICL site for the control or repaired plasmid. Single arrows indicate the progression of the leading strand to the ICL for the crosslinked plasmid. The strand size is shown above each product. (B) Mapping of leading strand progression for pTUC and pTUC-PSO after 65 min of incubation in Xenopus egg extracts in the continuous presence of [α-³²P]-dATP. Plasmids were digested by the indicated enzymes and analyzed on 10% polyacrylamide denaturing gel. Faint bands visible in lanes 3 and 4 likely result from a star activity of Sac II. The two 28 nt size indicators are at two different positions due to gel smiling. (C) Mapping of leading strand progression for pTUC and pTUC-PSO at 25, 35, 50, 65, 85, 95, 120 and 180 min. Plasmids were digested with EcoRI and BamHI and subjected to migration on a 10% polyacrylamide denaturing gel. 28 nt and 46 nt fragments correspond to the DNA size expected for the leading strand arriving at the psoralen from the EcoRI side or BamHI side, respectively.</p

Model for psoralen ICL repair in Xenopus egg extract.

<p>During replication of plasmid DNA containing a single psoralen ICL, replication forks stall at the ICL advancing up to 1 nt from the lesion. Coordinated incisions of one parental strand around the lesion can occur whether one (right) or both (left) forks have stalled, resulting in unhooking of the lesion. Next, translesion synthesis occurs across the unhooked psoralen adduct and other events implying HR and/or NER regenerate two repaired duplexes as proposed elsewhere <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0018554#pone.0018554-Muniandy1" target="_blank">[5]</a>. Both incision events and subsequent processing of the broken replication intermediates are stimulated by the ATR-Chk1 pathway.</p

TFO and purification of monomodified plasmid.

<p>(A) Structure of the TFO linked in 3′ to 4, 5′, 8-trimethylpsoralen and in 5′ to biotin. (B) Localization of the TFO binding site and position of the psoralen ICL on pTUC plasmid. P and A are schematic representations of primers for q-PCR used in (D). P primers surround the psoralen ICL site and amplify a region of 113 nt, the A primers amplify an undamaged regions of 129 nt. (C) Analysis of the crosslinked plasmid after UV irradiation and before (input) or after (purified) DTT elution from a strepatvidin column. DNA was digested with BamHI + EcoRI and radioactively labelled before electrophoresis on a 10% polyacrylamide denaturing gel. Interpretative diagrams of the relevant molecular species are shown on lane sides. (D) Input and purified plasmids were subjected to q-PCR with primers P and A. Mean values of 3 q-PCRs for the input and 12 q-PCRs for the purified plasmid are presented. For calculation details see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0018554#s4" target="_blank">Material and Methods</a>. (E) After purification pTUC-PSO was analyzed on a 0.8% agarose gel TBE 1x alongside with control plasmid and a molecular weight ladder.</p

Sequence-Specific Base Pair Mimics Are Efficient Topoisomerase IB Inhibitors

Topoisomerase IB controls DNA topology by cleaving DNA transiently. This property is used by inhibitors, such as camptothecin, that stabilize, by inhibiting the religation step, the cleavage complex, in which the enzyme is covalently attached to the 3′-phosphate of the cleaved DNA strand. These drugs are used in clinics as antitumor agents. Because three-dimensional structural studies have shown that camptothecin derivatives act as base pair mimics and intercalate between two base pairs in the ternary DNA–topoisomerase–inhibitor complex, we hypothesized that base pairs mimics could act like campthotecin and inhibit the religation reaction after the formation of the topoisomerase I–DNA cleavage complex. We show here that three base pair mimics, nucleobases analogues of the aminophenyl-thiazole family, once targeted specifically to a DNA sequence were potent topoisomerase IB inhibitors. The targeting was achieved through covalent linkage to a sequence-specific DNA ligand, a triplex-forming oligonucleotide, and was necessary to position and keep the nucleobase analogue in the cleavage complex. In the absence of triplex formation, only a weak binding to the DNA and topoisomerase I-mediated DNA cleavage was observed. The three compounds were equally active once conjugated, implying that the intercalation of the nucleobase upon triplex formation is the essential feature for the inhibition activity

Quantification of topo II-mediated DNA cleavage in the presence of TFO–drug conjugates

<p><b>Copyright information:</b></p><p>Taken from "Molecular basis of the targeting of topoisomerase II-mediated DNA cleavage by VP16 derivatives conjugated to triplex-forming oligonucleotides"</p><p>Nucleic Acids Research 2006;34(6):1900-1911.</p><p>Published online 5 Apr 2006</p><p>PMCID:PMC1447649.</p><p>© The Author 2006. Published by Oxford University Press. All rights reserved</p> The analysis was as in and the gels were quantified after normalization relative to total radioactivity loaded. () Scheme showing the enhanced cleavage site of each conjugate: the 5′ conjugates are depicted in green as the corresponding cleavage site a; the 3′ 16TFO conjugates are depicted in red as the corresponding cleavage site f; the 3′ 20TFO conjugates are depicted in blue as the corresponding cleavage site g. The other topo II-mediated DNA cleavage sites described in the text are also labeled with letters. () Quantification of the specific cleavage for 20TFO-L- on both strands compared to free 20TFO-L. The cleavage intensity was normalized to the cleavage intensity of the free drug (at 1 µM) on a logarithmic scale at each cleavage site. The oligopyrimidine strand is in gray and the oligopurine strand is in black, the conjugate in filled bars and the 20TFO-L alone in hatched bars. () Specific cleavage intensities of the conjugates on the oligopyrimidine-containing strand of the duplex (Y). The 5′ 16TFO conjugates are depicted in light green (hatched bars -L-16TFO, squares -L-16TFO, horizontal bars -L-16TFO, vertical bars -L-16TFO), the 5′ 20TFO conjugates are depicted in dark green (hatched bars -L-20TFO, vertical bars -L-20TFO), the 3′ 16TFO conjugates are in red [hatched bars 16TFO-L-, squares 16TFO-L-, horizontal bars 16TFO-L-, vertical bars 16TFO-L-, crosses 16TFO-L-(4)] and the 3′ 20TFO ones are in blue [hatched bars 20TFO-L-, vertical bars 20TFO-L-, crosses 20TFO-L-(4), dots 20TFO-L-(4)]

The sequence of the target duplex and the TFOs, and the chemical structure of the drug–TFO conjugates

<p><b>Copyright information:</b></p><p>Taken from "Molecular basis of the targeting of topoisomerase II-mediated DNA cleavage by VP16 derivatives conjugated to triplex-forming oligonucleotides"</p><p>Nucleic Acids Research 2006;34(6):1900-1911.</p><p>Published online 5 Apr 2006</p><p>PMCID:PMC1447649.</p><p>© The Author 2006. Published by Oxford University Press. All rights reserved</p> The 77 bp duplex target sequence was inserted between the BamHI and EcoRI sites of pBSK. The TFO is complementary to the oligopurine strand of the duplex and binds parallel to it. The target site is in boldface for the 20 nt TFO and is underlined for the 16 nt TFOs. , 5-methyl-2′-deoxycytidine; , 5-propynyl-2′-deoxyuridine. The structures of the VP16 derivatives-TFO conjugates used in this study are shown. The nomenclature of the conjugates is described in the Materials and Methods

Identification of Novel Inhibitors of DNA Methylation by Screening of a Chemical Library

In order to discover new inhibitors of the DNA methyltransferase 3A/3L complex, we used a medium-throughput nonradioactive screen on a random collection of 1120 small organic compounds. After a primary hit detection against DNA methylation activity of the murine Dnmt3A/3L catalytic complex, we further evaluated the EC₅₀ of the 12 most potent hits as well as their cytotoxicity on DU145 prostate cancer cultured cells. Interestingly, most of the inhibitors showed low micromolar activities and little cytotoxicity. Dichlone, a small halogenated naphthoquinone, classically used as pesticide and fungicide, showed the lowest EC₅₀ at 460 nM. We briefly assessed the selectivity of a subset of our new inhibitors against hDNMT1 and bacterial Dnmts, including M. SssI and EcoDam, and the protein lysine methyltransferase PKMT G9a and the mode of inhibition. Globally, the tested molecules showed a clear preference for the DNA methyltransferases, but poor selectivity among them. Two molecules including Dichlone efficiently reactivated YFP gene expression in a stable HEK293 cell line by promoter demethylation. Their efficacy was comparable to the DNMT inhibitor of reference 5-azacytidine

Synthesis and Evaluation of Analogues of <i>N</i>‑Phthaloyl‑l‑tryptophan (RG108) as Inhibitors of DNA Methyltransferase 1

DNA methyltransferases (DNMT) are promising drug targets in cancer provided that new, more specific, and chemically stable inhibitors are discovered. Among the non-nucleoside DNMT inhibitors, <i>N</i>-phthaloyl-l-tryptophan <b>1</b> (RG108) was first identified as inhibitor of DNMT1. Here, <b>1</b> analogues were synthesized to understand its interaction with DNMT. The indole, carboxylate, and phthalimide moieties were modified. Homologated and conformationally constrained analogues were prepared. The latter were synthesized from prolino­homotryptophan derivatives through a methodology based amino–zinc–ene–enolate cyclization. All compounds were tested for their ability to inhibit DNMT1 in vitro. Among them, constrained compounds <b>16</b>–<b>18</b> and NPys derivatives <b>10</b>–<b>11</b> were found to be at least 10-fold more potent than the reference compound. The cytotoxicity on the tumor DU145 cell line of the most potent inhibitors was correlated to their inhibitory potency. Finally, docking studies were conducted in order to understand their binding mode. This study provides insights for the design of the next-generation of DNMT inhibitors