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Sidney M Hecht

Publications and source records attributed to Sidney M Hecht.

At least 55 records · Page 3Linked to original sources
PubMed2004

Identification of small molecule synthetic inhibitors of DNA polymerase beta by NMR chemical shift mapping.

DNA polymerase beta (beta-pol) plays a central role in repair of damaged DNA bases by base excision repair (BER) pathways. A predominant phenotype of beta-pol null mouse fibroblasts is hypersensitivity to the DNA-methylating agent methyl methanesulfonate. Residues in the 8-kDa domain of beta-pol that seem to interact with a known natural product beta-pol inhibitor, koetjapic acid, were identified by NMR chemical shift mapping. The data implicate the binding pocket as the hydrophobic cleft between helix-2 and helix-4, which provides the DNA binding and deoxyribose phosphate lyase activities of the enzyme. Nine structurally related synthetic compounds, containing aromatic or other hydrophobic groups in combination with two carboxylate groups, were then tested. They were found to bind to the same or a very similar region on the surface of the enzyme. The ability of these compounds to potentiate methyl methanesulfonate cytotoxicity, an indicator of cellular BER capacity, in wild-type and beta-pol null mouse fibroblasts, was next ascertained. The most active and beta-pol-specific of these agents, pamoic acid, was further characterized and found to be an inhibitor of the deoxyribose phosphate lyase and DNA polymerase activities of purified beta-pol on a BER substrate. Our results illustrate that NMR-based mapping techniques can be used in the design of small molecule enzyme inhibitors including those with potential use in a clinical setting.

Animals↗
PubMed2004

Identification of specific nonbridging phosphate oxygens important for DNA cleavage by human topoisomerase I.

Methylphosphonate-bearing oligonucleotides are characterized by the replacement of one of the nonbridging oxygen atoms with a methyl group. While neutralizing the negative charge associated with the phosphodiester at the point of substitution, the methyl group also imparts chirality to the phosphorus atom. Herein we report the synthesis of a number of oligonucleotides containing isomerically pure S(p) and R(p) methylphosphonates at single positions for the purpose of investigating the hydrogen-bonding contacts necessary for human topoisomerase I function. It was possible to correlate these data to the recent X-ray crystal structure of a truncated form of the enzyme and demonstrate a severe decrease of cleavage efficiency when any of the nonbridging oxygen atoms upstream from the cleavage site was removed. Also observed was increased cleavage for oligonucleotides substituted with methylphosphonates downstream from the cleavage site. These effects were shown to be due primarily to alteration of the binding of the modified DNA substrates by human DNA topoisomerase I.

Base Pairing↗
PubMed2004

Synthesis and biochemical properties of E-ring modified luotonin A derivatives.

Luotonin A is a cytotoxic pyrroloquinazolinoquinoline alkaloid that has been shown to stabilize the human topoisomerase I-DNA covalent binary complex in the same fashion as the antitumor alkaloid camptothecin. A study of the structural elements in luotonin A required for binary complex stabilization has revealed key differences relative to those required for camptothecin.

Enzyme Inhibitors↗
PubMed2004

Camptothecin: current perspectives.

This review provides a detailed discussion of recent advances in the medicinal chemistry of camptothecin, a potent antitumor antibiotic. Two camptothecin analogues are presently approved for use in the clinic as antitumor agents and several others are in clinical trials. Camptothecin possesses a novel mechanism of action involving the inhibition of DNA relaxation by DNA topoisomerase I, and more specifically the stabilization of a covalent binary complex formed between topoisomerase I and DNA. This review summarizes the current status of studies of the mechanism of action of camptothecin, including topoisomerase I inhibition and additional cellular responses. Modern synthetic approaches to camptothecin and several of the semi-synthetic methods are also discussed. Finally, a systematic evaluation of novel and important analogues of camptothecin and their contribution to the current structure-activity profile are considered.

Animals↗
PubMed2004

Water-soluble camptothecin derivatives that are intrinsic topoisomerase I poisons.

[structure: see text] In an effort to improve the water solubility of camptothecin, four 20-O-phosphate and phosphonate analogues have been prepared. These analogues are freely water soluble, stable at physiological pH, and stabilize the human topoisomerase I-DNA covalent binary complex with the same sequence selectivity as camptothecin itself. All four compounds inhibited the growth of yeast expressing human topoisomerase I in an enzyme-dependent fashion.

Camptothecin↗
PubMed2004

Site- and subunit-specific incorporation of unnatural amino acids into HIV-1 reverse transcriptase.

A highly efficient cell-free translation system has been combined with suppressor tRNA technology to substitute nor-Tyr and 3-fluoro-Tyr in place of Tyr183 at the DNA polymerase active site of p66 of human immunodeficiency virus type 1 reverse transcriptase (HIV-1 RT). Supplementing the wild-type HIV-1 p51 RT subunit into this translation system permitted reconstitution of the biologically relevant p66/p51 heterodimer harboring Tyr analogs exclusively on the catalytically competent p66 subunit. Addition of an affinity tag at the p66 C-terminus allowed rapid, one-step purification of reconstituted and selectively mutated heterodimer HIV-1 RT via strep-Tactin-agarose affinity chromatography. The purified enzyme was demonstrated to be free of contaminating nucleases, allowing characterization of the DNA polymerase and ribonuclease H activities associated with HIV-1 RT. Preliminary characterization of HIV-1 RT(nor-Tyr) and HIV-1 RT(m-fluoro-Tyr) is presented. The success of this strategy will facilitate detailed molecular analysis of structurally and catalytically critical amino acids via their replacement with closely related, unnatural analogs.

Amino Acid Substitution↗
PubMed2004

Remote phosphate contacts trigger assembly of the active site of DNA topoisomerase IB.

Vaccinia topoisomerase IB forms a covalent DNA-(3'-phosphotyrosyl)-enzyme intermediate at its target site 5'-CCCTTp downward arrow in duplex DNA. The contributions of backbone electrostatics and individual phosphate oxygens to the transesterification reaction were probed by introducing 22 single Rp and Sp methylphosphonate diastereomers at 11 positions flanking the cleavage site. Methyl groups at eight positions (four on the scissile strand and four on the nonscissile strand) inhibited the rate of single-turnover cleavage by factors of 50-50,000. Stereospecific interference was observed at several phosphates, thereby distinguishing simple electrostatic contributions from putative specific polar contacts to either the pro-Sp or pro-Rp oxygens. The functionally relevant phosphate oxygens are located on the minor groove face of the helix on which the scissile phosphodiester resides. Our findings, combined with available crystal structures of vaccinia and human topoisomerase IB, show how specific phosphate contacts remote from where chemistry occurs are critical for assembly of the active site.

Base Sequence↗
PubMed2004

New neolignans that inhibit DNA polymerase beta lyase.

Bioassay-directed fractionation of a methyl ethyl ketone extract of the roots of Endlicheria aff. resulted in the isolation of four new neolignans (1-4) and eight known compounds, namely, canellin A (5), canellin C (6), 3'-methoxyguianin (7), (7S,8R,1'S,5'S,6'R)-Delta(2',8')-3',6'-dihydroxy-5'-methoxy-3,4-methylenedioxy-4'-oxo-8.1',7.5'-neolignan (8), armenin-B (9), dillapiole (10), 1-allyl-2,6-dimethoxy-3,4-methylenedioxybenzene (11), and omega-hydroxyisodillapiole (12). The structures of the new compounds (1-4) were established as (7S,8R,1'S,5'S,6'R)-Delta(2',8')-5',6'-dihydroxy-3'-methoxy-3,4-methylenedioxy-4'-oxo-8.1',7.5'-neolignan, (7S,8R,1'S,5'S,6'R)-Delta(2',8')-3',5',6'-trihydroxy-3,4-methylenedioxy-4'-oxo-8.1',7.5'-neolignan, 2,4-dimethoxy-5,6-methylenedioxy-1-(2-propenyl)benzene, and 2,6-dimethoxy-3,4-methylenedioxycinnamyl alcohol, respectively, on the basis of spectroscopic interpretation.

DNA Polymerase beta↗
PubMed2004

A new ursane triterpene from Monochaetum vulcanicum that inhibits DNA polymerase beta lyase.

Bioassay-directed fractionation of a butanone extract of Monochaetum vulcanicum resulted in the isolation of a new triterpene (1) and four known compounds, ursolic acid (2), 2alpha-hydroxyursolic acid (3), 3-(p-coumaroyl)ursolic acid (4), and beta-sitosteryl-beta-d-galactoside (5). The structure of the new compound 1 was established as 3beta-acetoxy-2alpha-hydroxyurs-12-en-28-oic acid on the basis of extensive 1D and 2D NMR spectroscopic interpretation and chemical derivatization. Compounds 1-3 and 5 exhibited polymerase beta lyase activity.

Acetylation↗
PubMed2004

A DNA-damaging oxoaporphine alkaloid from Piper caninum.

Bioassay-guided fractionation of an active organic extract of Piper caninum, using a sensitive yeast assay to monitor putative double-strand DNA-damaging activity, resulted in the isolation of the 4,5-dioxoaporphine alkaloid cepharadione A (1). Compound 1 exhibited potent inhibitory activity in a yeast cytotoxicity assay with IC(50) values of 50.2 nM toward RS321NpRAD52 grown on glucose versus 293 nM toward the same yeast strain grown on galactose.

Alkaloids↗
PubMed2004

DNA polymerase beta lyase inhibitors from Maytenus putterlickoides.

During a survey of plant secondary metabolites for DNA polymerase beta lyase inhibitors, we found that a crude methyl ethyl ketone extract prepared from Maytenus putterlickoides showed strong inhibition of the lyase activity of DNA polymerase beta in an in vitro assay. Bioassay-guided fractionation of the extract, using an in vitro assay, resulted in the discovery of a new active principle, 30-(4'-hydroxybenzoyloxy)-11alpha-hydroxylupane-20(29)-en-3-one (1), as well as a known compound, (-)-epicatechin (2). Compounds 1 and 2 exhibited DNA polymerase beta lyase inhibitory activity with IC50 values of 62.8 and 18.5 microM, respectively. Compound 2 was capable of potentiating the action of the monofunctional methylating agent methyl methanesulfonate in cultured human cancer cells, consistent with the possible utility of inhibitors of this type in vivo.

Antineoplastic Agents, Phytogenic↗
PubMed2004

Biscoumarin derivatives from Edgeworthia gardneri that inhibit the lyase activity of DNA polymerase beta.

Bioassay-guided fractionation of an active methyl ethyl ketone extract of Edgeworthia gardneri, using an assay to monitor DNA polymerase beta lyase inhibition, resulted in the isolation of three known biscoumarin derivatives, 7-hydroxy-3,7'-dicoumaryl ether (edgeworin, 1), 7-hydroxy-6-methoxy-3,7'-dicoumaryl ether (daphnoretin, 2), and 6,7-dihydroxy-3,7'-dicoumaryl ether (edgeworthin, 3). Compounds 1-3 inhibited the lyase activity of DNA polymerase beta with IC(50) values of 7.3 microg/mL (22.5 microM), 43.0 microg/mL (122.3 microM), and 32.1 microg/mL (94.8 microM), respectively.

Bhutan↗
PubMed2004

A coumarin from Mallotus resinosus that mediates DNA cleavage.

A crude extract prepared from roots of Mallotus resinosus exhibited significant Cu(2+)-dependent DNA strand scission activity and was thus selected for bioassay-guided fractionation. Scopoletin (1), a simple coumarin, was identified as the active principle responsible for DNA cleavage activity of the crude extract. The DNA strand scission activity of 1, as well as that of three structural analogues, is reported.

Coumarins↗
PubMed2004

Marine sesquiterpenoids that inhibit the lyase activity of DNA polymerase beta.

Bioassay-directed fractionation of an extract of the marine species Spongia sp. led to the discovery of the new sesquiterpenoid derivative 17-O-isoprenyldictyoceratin-C (1), the known sesquiterpenoid derivative dictyoceratin-C (2), and the sesquiterpenoid quinone ilimaquinone (3), in addition to the nucleoside 2'-deoxyuridine. The structure of the new compound 1 was determined on the basis of spectroscopic methods and by conversion of dictyoceratin-C (2) to 1.

Animals↗
PubMed2003

Solid-phase synthesis and biochemical evaluation of conformationally constrained analogues of deglycobleomycin A5.

Deglycobleomycin binds to and degrades the self-complementary oligonucleotide d(CGCTAGCG)(2) in a sequence selective fashion. A previous modeling study [J. Am. Chem. Soc. 120, (1998), 7450] had shown that, during binding to double stranded DNA, the conformation of the methylvalerate domain of deglycoBLM approximated that of S-proline. In the belief that an analogue of deglycoBLM structurally constrained to mimic the DNA-bound conformation might exhibit facilitated DNA binding and cleavage, an analogue of deglycoBLM was prepared in which the methylvalerate moiety was replaced by S-proline. This deglycoBLM analogue, as well as the related analogue containing R-proline, was synthesized on a TentaGel resin. Both of the analogues were found to be capable of binding Fe(2+) and activating O(2) for transfer to styrene. However, both deglycoBLM analogues exhibited diminished abilities to effect the relaxation of supercoiled plasmid DNA, and neither mediated sequence selective DNA cleavage.

Bleomycin↗
PubMed2003

Luotonin A. A naturally occurring human DNA topoisomerase I poison.

Luotonin A is a pyrroloquinazolinoquinoline alkaloid isolated from the Chinese herbal medicinal plant Peganum nigellastrum. Although previously shown to exhibit cytotoxicity against the murine leukemia P-388 cell line, the mechanism of action of luotonin A is unknown. Presently, we demonstrate that luotonin A stabilizes the human DNA topoisomerase I-DNA covalent binary complex, affording the same pattern of cleavage as the structurally related topoisomerase I inhibitor camptothecin. Luotonin A also mediated topoisomerase I-dependent cytotoxicity toward Saccharyomyces cerevisiae lacking yeast topoisomerase I, but harboring a plasmid having the human topoisomerase I gene under the control of a galactose promoter. This finding identifies a putative biochemical locus for the cytotoxic action of luotonin A and has important implications for the mechanism of action of camptothecin and the design of camptothecin analogues.

Alkaloids↗
PubMed2003

3'-modified oligonucleotides by reverse DNA synthesis.

Reverse DNA oligonucleotide synthesis (i.e. from 5'-->3') is a strategy that has yet to be exploited fully. While utilized previously for the construction of alternating 3'-3'- and 5'-5'-linked antisense oligonucleotides, the use of nucleoside 5'-phosphoramidites has not generally been used for the elaboration of (modified) oligonucleotides. Presently, the potential of reverse oligonucleotide synthesis for the facile synthesis of 3'-modified DNAs is illustrated using a phosphoramidite derived from tyrosine. The derived oligonucleotide was shown to have chromatographic and electrophoretic properties identical with the modified oligonucleotide resulting from the proteinase K digestion of the vaccinia topoisomerase I-DNA covalent complex. The results confirm the nature of the structure previously assigned to this product, and establish the facility with which proteinase K is able to complete the digestion of the polypeptide backbone of the DNA oligonucleotide-linked topoisomerase I.

DNA↗