The Effects of DNA Covalent Adducts on in Vitro Transcription

Experimental and theoretical investigation on the nonlinear optical properties of LDS 821 dye in different solvents and DNA

Linear and nonlinear optical properties of near-infrared laser grade dye LDS 821 in different solvents and Salmon Deoxyribonucleic acid (DNA) were studied using spectroscopic and Z-scan techniques. UV-Vis absorption spectrum of the dye shows a bathochromic shift with a decrease in the solvent polarity parameter, and in DNA, the dye exhibits a hypochromic shift. The fluorescence spectrum of the dye does not show any notable correlation with the solvent polarity parameter, but in DNA, the fluorescence intensity of the dye decreases with the incremental addition of DNA. Molecular docking studies reveal that the dye intercalates on the major grooves of DNA. Nonlinear optical properties of the dye in different solvents and phosphate buffer solution with varying DNA concentrations were studied using the Z-scan technique using a Q-switched Nd: YAG laser operating at fundamental and second harmonics. A closed and open aperture Z-scan of dye in different solvents was carried out to estimate the nonlinear refractive index, excited-state absorption cross-section, and two-photon absorption coefficient (TPA). The variation in nonlinear optical properties of the dye in different solvents was due to solvent-induced structural modifications. Theoretical investigation on nonlinear optical properties of the dye in different solvents was carried out using density function theory. The theoretical first and second-order hyperpolarizability was calculated using B3LYP functional. The predicated nonlinear optical parameters of the dye in different solvents does not show any direct correlation with solvent polarity. Nonlinear absorption of the dye in phosphate buffer solution (PBS) and DNA were estimated. The nonlinear absorption of the dye in PBS decreases with the addition of DNA. Molecular docking studies were carried out to determine the structural changes induced in dye due to the intercalation with DNA.

Hydrogen peroxide activated quinone methide precursors with enhanced DNA cross-linking capability and cytotoxicity towards cancer cells

Quinone methide (QM) formation induced by endogenously generated H₂O₂ is attractive for biological and biomedical applications. To overcome current limitations due to low biological activity of H₂O₂-activated QM precursors, we are introducing herein several new arylboronates with electron donating substituents at different positions of benzene ring and/or different neutral leaving groups. The reaction rate of the arylboronate esters with H₂O₂ and subsequent bisquinone methides formation and DNA cross-linking was accelerated with the application of Br as a leaving group instead of acetoxy groups. Additionally, a donating group placed meta to the nascent exo-methylene group of the quinone methide greatly improves H₂O₂-induced DNA interstrand cross-link formation as well as enhances the cellular activity. Multiple donating groups decrease the stability and DNA cross-linking capability, which lead to low cellular activity. A cell-based screen demonstrated that compounds 2a and 5a with a OMe or OH group dramatically inhibited the growth of various tissue-derived cancer cells while normal cells were less affected. Induction of H2AX phosphorylation by these compounds in CLL lymphocytes provide evidence for a correlation between cell death and DNA damage. The compounds presented herein showed potent anticancer activities and selectivity, which represent a novel scaffold for anticancer drug development.

Rate-adjusted cross-linking reaction by photoresponsive α-bromoaldehyde (PBA)-conjugated ODN

We developed a photoresponsive α-bromoaldehyde-conjugated oligonucleotide (PBA-ODN). The PBA-ODN selectively reacted and formed covalent bonds with target oligonucleotides having adenine or cytosine at the frontal position of the aldehyde derivative. Kinetic studies revealed that PBA-ODN has increased kinetic rates for the formation of cross-linked duplexes compared with the corresponding α-chloroaldehyde-conjugated oligonucleotide (PCA-ODN).

Exploring the strength, mode, dynamics, and kinetics of binding interaction of a cationic biological photosensitizer with DNA: implication on dissociation of the drug-DNA complex via detergent sequestration

The present study aims at exploring a detailed characterization of the binding interaction of a promising cancer cell photosensitizer, harmane (HM), with DNA extracted from herring sperm. The polarity-sensitive prototropic transformation of HM, a naturally occurring, fluorescent, drug-binding alkaloid, β-carboline, is remarkably modified upon interaction with DNA and is manifested through significant modulations on the absorption and emission profiles of HM. From the series of studies undertaken in the present program, for example, absorption; steady-state emission; the effect of chaotrope (urea); iodide ion-induced steady-state fluorescence quenching; circular dichroism (CD); and helix melting from absorption spectroscopy; the mode of binding of HM into the DNA helix has been substantiated to be principally intercalative. Concomitantly, a discernible dependence of the photophysics of the DNA-bound drug on the medium ionic strength indicates that electrostatic attraction should not be ignored in the interaction. Efforts have also been delivered to delineate the dynamical aspects of the interaction, such as modulation in time-resolved fluorescence decay and rotational relaxation dynamics of the drug within the DNA environment. In view of the prospective biological applications of HM, the issue of facile dissociation of intercalated HM from the DNA helix also comprises a crucial prerequisite for the functioning as an effective therapeutic agent. In this context, our results imply that the concept of detergent-sequestered dissociation of the drug from the drug-DNA complex can be a prospective strategy through an appropriate choice of the detergent molecule. The utility of the present work resides in exploring the potential applicability of the fluorescence property of HM for studying its interactions with a relevant biological target, for example, DNA. In addition, the methods and techniques used in the present work can also be exploited to study the interaction of HM with other biological, biomimicking assemblies and drug delivery vehicles, and so forth.

BINOL-amino acid conjugates as triggerable carriers of DNA-targeted potent photocytotoxic agents

Mild photoactivation of new BINOL-amino acid and -amino ester conjugates (BINOLAMs) yielded alkylating and DNA cross-linking agents with high photoefficiency and superior cytotoxicity. Detection of the transient electrophile, by laser flash photolysis (LFP), suggests that BINOL-quinone methides (QMs) are key intermediates in the process. QMs trapping by water, monitored in a time-dependent product distribution analysis, demonstrated that the phototriggered reactivity of BINOLAMs as bis-alkylating agents is the result of a two-step process involving sequential photogeneration of monoalkylating QMs. Light activation of the BINOL-L-amino esters produced cytotoxic QMs very effective against human tumor LoVo cells with EC50 in the 130-230 nM range. Trimethylpsoralen (PS) is about 4 times less potent than our newly tested compounds. BINOL-L-proline methyl ester showed notable photoselectivity because it displayed cytotoxic effects upon irradiation only and was able to efficiently reach the target DNA inside the cells, where it forms both alkylated and cross-linked species.

Photoreaction of [Ru(hat)2phen]2+ with guanosine-5'-monophosphate and DNA: formation of new types of photoadducts

[Ru(hat)2phen]2+ (HAT=1,4,5,8,9,12-hexaazatriphenylene, phen=1,10-phenanthroline) interacts with a good affinity with polynucleotides and DNA by intercalation, despite the presence of a second voluminous ancillary HAT ligand. It photoreacts with guanosine-5'-monophosphate (GMP). From HPLC, ESMS and NMR analyses, it can be concluded that this complex forms photoadducts with GMP. In contrast to the photoadducts isolated with Ru-TAP complexes (TAP=1,4,5,8-tetraazaphenanthrene), the photoadducts with [Ru(hat)2phen]2+ contain a covalent link between the oxygen atom of the guanine unit and a HAT ligand. Formation of oxidised photoadducts and compounds resulting from the addition of two GMP entities to the complex are also detected as side products. In the presence of oligo- and polynucleotides, [Ru(hat)2phen]2+ yields photoadducts when guanine bases are present.

[N-ethyl- and [N,N'-diethyl-1,2-bis(2,6-difluoro-3-hydroxyphenyl)-ethylenediamine]dichloroplatinum(II): structure and cytotoxic/estrogenic activity in breast cancer cells

N-Ethyl and N,N'-diethyl derivatives (erythro- and threo-2-PtCl2; meso- and D,L-3-PtCl2) of [meso- and [D,L-1,2-bis(2,6-difluoro-3-hydroxyphenyl)ethylenediamine]dichloroplatinum(II) (meso- and D,L-1-PtCl2) were synthesized and tested for cytotoxicity on the estrogen receptor-positive (ER+) human MCF-7 breast cancer cell line. In this test, only D,L-1-PtCl2 and threo-2-PtCl2 showed strong cytotoxic properties. This revealed the existence of at least one NH2 fragment as a prerequisite for antitumor activity. Furthermore, studies on the three-dimensional structure of the new compounds demonstrated that the aryl and alkyl residues at the five-membered chelate ring have to be arranged in equatorial positions for the triggering of cytotoxic effects, very likely due to the reaction with d(GpG) sequences in DNA resulting in GG-N7,N7 chelates. A contribution of the ER-mediated processes--(a) hindrance of the cellular processing of Pt-modified DNA by overexpression of high mobility group domain proteins and (b) interruption of the vicious circle of mutual growth stimulation of breast cancer cells and granulocytes/macrophages by reduction of the formation of key cytokines--to the anti-breast cancer activity of threo-2-PtCl2 is unlikely, since we did not observe transcription activation in the test on ER+ MCF-7 breast cancer cells stably transfected with luciferase reporter plasmid ERE(wtc)luc.

Structure???anti-leukemic activity relationship study of B- and D-ring modified and non-modified steroidal esters of chlorambucil??s active metabolite

We have studied the effect of modification of the B-steroidal ring to lactamic on the anti-leukemic potency of D-modified and D-non-modified steroidal esters of chlorambucil's active metabolite. The compounds synthesized were studied against leukemias P388 and L1210 after the subsequent estimation of their toxicity in vivo, and for their ability to induce sister chromatid exchanges (SCEs) and to inhibit cell proliferation in normal human lymphocytes in vitro. The in vitro results correlated well, on a molar basis, with the results obtained from the study of the anti-leukemic potency. In a comparative study, the B-lactamic steroidal derivatives proved less active than the 7-oxidized ones against both leukemias. The presence of the -NHCO- group in the B-steroidal ring did not have the same positive effect on the biological action of chlorambucil's active metabolite esters as in the D-lactamic ring. However, this new modification of the B-ring rendered the final esteric derivatives much more toxic, compared with to the corresponding esters with a simple B-ring. This loss of the anti-leukemic specificity, which occurs from the modification of the B-ring, is additional evidence for the role of the steroidal part on the mechanism of action of these promising compounds. This provides support for the notion that the steroidal part of these molecules is not just a simple biological carrier, as has been speculated for many years.

Effects of anticancer drugs on transcription factor–DNA interactions

DNA-interacting anticancer drugs are able to affect the propensity of DNA to interact with proteins through either reversible binding or covalent bond formation. The effect of the drugs on transcription factor interactions with DNA is reviewed. These effects can be classified as (i) competition between a drug and regulatory protein for target sequences; (ii) weakening of this interaction; (iii) enhancement of this interaction by chemical modification of the DNA and the creation of non-natural binding sites; and (iv) a 'suicide' mechanism, which is observed when a transcription factor induces changes in DNA structure, allowing a drug to bind to a target sequence. Several new strategies -- the antigene approach with oligonucleotides, peptide nucleic acids or locked nucleic acids, and sequence-specific polyamides -- are also reviewed.

Modified oligonucleotides containing lithocholic acid in their backbones: their enhanced cellular uptake and their mimicking of hairpin structures

Their enhanced cell permeability and their ability to mimic DNA structures make modified oligodeoxyribonucleotides (ODNs) very important substances for increasing our understanding of cell biology and for therapeutic applications. Lithocholic acid is a hydrophobic secondary bile acid that is a substrate of nuclear Pregnane X receptor (PXR). We designed and synthesized novel lithocholic acid-based ODNs (L-ODNs) by using a new phosphoramidite derived from lithocholic acid. By comparing data obtained from circular-dichroism, melting-point, and theoretical studies, we believe that these L-ODNs adopt DNA hairpin structures. Furthermore, L-ODNs have enhanced cellular uptake properties with respect to regular ODNs. To demonstrate their enhanced cell permeabilities, we carried out cellular uptake experiments of L-ODNs in HeLa cells. By attaching fluorescein as a fluorescence label and using confocal microscopy, we observed that the permeability of L-ODNs is much higher than that of natural ODNs.

Interstrand Cross-Linking of DNA by FK317 and Its Deacetylated Metabolites FR70496 and FR157471

FR900482 (1) and FR66979 (2) are structurally novel natural products isolated by Fujisawa in 1987 and have been shown to be highly potent antitumor antibiotics structurally related to the mitomycins. Studies on the mode of action have established that these new agents form covalent DNA interstrand cross-links both in vitro and in vivo as a result of the reactive mitosene intermediate generated upon bioreductive activation. Semisynthetic analogues such as FK973 (3) and FK317 (4) were developed in the search for potentially superior clinical candidates. Although FK317 has been shown to be a potent compound, to date no direct evidence of DNA interstrand cross-link sequence specificity has been reported. In this study, DNA interstrand cross-links were generated by treatment of a synthetic duplex DNA substrate with FK317 (4) and its deacetylated metabolites FR70496 (5) and FR157471 (6). Analysis by gel electrophoresis revealed the formation of orientation isomers displaying electrophoretic mobility vastly greater than the mobilities of those generated from FR900482 (1). Despite these differences, it was established by Fe(II)-EDTA footprinting that FK317 (4) as well as 5 and 6 forms DNA interstrand cross-links within the expected 5'CpG3' step, clearly demonstrating that the phenolic hydrogen in 1 and 2 is not a prerequisite for efficient DNA interstrand cross-linking by the FR class of compounds.

Synthesis and characterization of pi-stacked phenothiazine-labeled oligodeoxynucleotides

[reaction: see text] A facile procedure for the incorporation of N-methyl phenothiazine as the terminal nucleoside in oligodeoxynucleotides is reported. The phenothiazine nucleoside analogue is synthesized and then incorporated into DNA using an automated DNA solid-phase synthesizer. Phenothiazine-labeled oligodeoxynucleotides form stable B-form duplexes with higher melting temperatures compared to unlabeled DNA duplexes.

Synthesis, characterization and antitumor studies of transition metal complexes of o-hydroxydithiobenzoate

o-Hydroxydithiobenzoate (o-HOdtb) forms complexes, [Ni(o-HOdtb)(o-HOdtbS)], [Cu(o-Odtb)], [Co(o-HOdtb)(3)], [Fe(2)(o-Odtb)(3)], [Bu(n)(4)N][V(o-Odtb)(3)] and [Bu(n)(4)N][Zn(o-HOdtb)(3)] which were characterized by analyses and physicochemical studies. The bonding sites of o-HOdtb and the geometry of the complexes were determined by magnetic susceptibility, IR, ESR, NMR, Mössbauer and electronic spectral data. The structure of [Bu(n)(4)N][Zn(o-HOdtb)(3)] and H(2)C(o-HOdtb)(2) were assigned by single crystal X-ray diffraction studies. The monomeric complex [Bu(n)(4)N][Zn(o-HOdtb)(3)] crystallizes in Pna2(1) space group. The Mössbauer spectra of [Fe(2)(o-Odtb)(3)] at 298 and 80K suggest the presence of high spin iron(III) with an S=5/2 state. All the metal complexes were observed to inhibit the growth of tumor in vitro, whereas, ligand did not. In vivo administration of these complexes resulted in prolongation of survival of tumor-bearing mice. Tumor bearing mice administered with metal complexes showed reversal of tumor growth associated induction of apoptosis in lymphocytes. The paper discusses the possible mechanisms and therapeutic implication of the ligand and its metal complexes in tumor regression and tumor growth associated immunosuppression.

Mutagenicity of electrophilic N-acyloxy-N-alkoxyamides

N-acyloxy-N-alkoxybenzamides are mutagenic in TA100 without the need for metabolic activation with S9. Electronic effects of substituents on both the benzamide ring in N-acetoxy-N-butoxybenzamides or the benzyloxy ring in N-acetoxy-N-benzyloxybenzamides do not influence mutagenicity levels. For N-benzoyloxy-N-benzyloxybenzamides, mutagenicity levels are inversely related to the electron-withdrawing effect of substituents on the benzoyloxy leaving group. Since reactivities increase with increasing electron-withdrawing effects, mutagenicity correlates with stability rather than reactivity of these mutagens. Hydrophobicity is the dominant factor controlling mutagenicity levels and data for all mutagens correlate with computed logP values with a lower dependence (h=0.22) than that recorded for indirect mutagens (h=1.0), except where a sterically demanding p-tert-butyl substituent or a naphthyl group is present. N-acetoxy-N-butoxynaphthamide exhibits a much higher level of mutagenicity than predicted by its logP value and activity may be ascribed to an intercalative binding process with DNA rather than straightforward hydrophobic binding in the major or minor groove. Since these are direct-acting mutagens, structural factors influence binding and reactivity towards DNA.

DNA damage by nitrogen mustard in a gene containing multiple Sp1-binding sites

The human cytochrome c(1) gene TATA-less promoter contains 10 Sp1-binding elements that regulate the activation of transcription of this gene. Quantitative PCR was used to show that nitrogen mustard induces DNA lesions within this Sp1-binding region following exposure of HeLa cells to clinical levels of the drug. Alkylation of the cytochrome c(1) gene in HeLa cells increased with reaction time up to 4 h following exposure to nitrogen mustard, with 50% of the lesions (approximately 0.8/kb) forming within 1 h. An Sp1 competition assay showed that nitrogen mustard inhibited the binding of Sp1 to the promoter region of the cytochrome c(1) gene in HeLa cells. These results show that nitrogen mustard-induced damage to Sp1-binding sites may contribute to the toxicity of this compound by interfering with the activation of specific genes.

Cytotoxic and DNA-damaging properties of N-[2-(dimethylamino)ethyl]acridine-4-carboxamide (DACA) and its analogues

An antitumor drug N-[2-(dimethylamino)ethyl]acridine-4-carboxamide (DACA) and its three close structural analogs N-[2-(hydroxyethylamino)ethyl]acridine-4-carboxamide (DACAH), N-[2-(dimethylamino)ethyl]-9-aminoacridine-4-carboxamide (amino-DACA), and N-[2-(hydroxyethylamino)ethyl]-9-aminoacridine-4-carboxamide (amino-DACAH) were studied for their ability to inhibit RNA synthesis in vitro and to form topoisomerase II-mediated DNA lesions in relation to cell-killing activity. All tested compounds induced chromatin lesions characteristic of topoisomerase II-blocking drugs (DNA breaks and DNA-protein cross-links) in treated cells, but were much less active than reference antileukemic acridine m-AMSA (4'-(9-acridinylamino)-methanesulfon-m-anisidide). The ability to form these lesions was dependent on the structure of the 4-carboxamide side-chain, which seems to be an important factor affecting the drug transport rate through cell membrane. A 4-carboxamide chain with an N-2-(dimethylamino)ethyl moiety resulted in more efficient transport through cell membranes, higher cytotoxicity, and DNA-damaging activity. The mode of action of acridine-4-carboxamides was further elucidated by their incubation with cells in the presence of antitopoisomerase II agents of a known mechanism of inhibition. These were: bisdioxopiperazine (ICRF-187), a catalytic inhibitor of topoisomerase II, and etoposide (VP-16), an inducer of a cleavable complex of the enzyme with DNA. The cytotoxicity of DACA and its analogs was not antagonized by preincubating cells with ICRF-187. All tested acridines protected cells against DNA breakage induced by VP-16, but the extent of protection varied significantly. Amino-DACA, which easily penetrates cell membrane, fully inhibited DNA break formation, whereas other analogs exhibited a low degree of protection when used at high concentration. Our results suggest that the acridine-4-carboxamides discussed here are poor topoisomerase II poisons and that this enzyme is not their main target.

Transcriptional template activity of covalently modified DNA

The transcriptional template activity of covalent modified DNA is compared. 8-Methoxypsoralen (MOP), 3,4'dimethyl-8-methoxypsoralen (DMMOP) and benzopsoralen (BP) forming with DNA covalent complexes upon UV irradiation and exhibiting preference to pyrimidines, mostly thymines, differ in their cross-linking potency. MOP and DMMOP form both monoadducts and diadducts while no cross-links are formed by BP. Nitracrine (NC) forms covalent complexes with DNA upon reductive activation with dithiothreitol exhibiting a preference to purines and low cross-linking potency. Semilogarithmic plots of the relative template activity against the number of the drugs molecules covalently bound per 10(3) DNA nucleotides fit to regression lines corresponding to one-hit inactivation characteristics. The number of drug molecules decreasing RNA synthesis to 37% differ from 0.25 to 1.26 depending on the template used and the base preference but no dependence on the cross-linking potency was found.