Defining GC-specificity in the minor groove: side-by-side binding of the di-imidazole lexitropsin to C-A-T-G-G-C-C-A-T-G.

BACKGROUND: Polyamide drugs, such as netropsin, distamycin and their lexitropsin derivatives, can be inserted into a narrow B-DNA minor groove to form 1:1 complexes that can distinguish AT base pairs from GC, but cannot detect end-for-end base-pair reversals such as TA for AT. In contrast, 2:1 side-by-side polyamide drug complexes potentially are capable of such discrimination. Imidazole (Im) and pyrrole (Py) rings side-by-side read a GC base pair with the Im ring recognizing the guanine side. But the reason for this specific G-Im association is unclear because the guanine NH2 group sits in the center of the groove. A 2:1 drug:DNA complex that presents Im at both ends of a GC base pair should help unscramble the issue of imidazole reading specificity. RESULTS: We have determined the crystal structure of a 2:1 complex of a di-imidazole lexitropsin (DIM), an analogue of distamycin, and a DNA decamer with the sequence C-A-T-G-G-C-C-A-T-G. The two DIM molecules sit antiparallel to one another in a broad minor groove, with their cationic tails widely separated. Im rings of one drug molecule stack against amide groups of the other. DIM1 rests against nucleotides C7A8T9G10 of strand 1 of the helix, whereas DIM2 rests against G14G15C16C17 on strand 2. All DIM amide nitrogens donate hydrogen bonds to N and O atoms on the floor of the DNA groove and, in addition, the two Im rings on DIM2 accept hydrogen bonds from guanine N2 amines, thereby providing specific reading. The guanine N2 amine can bond to Im on its own side of the groove, but not on the cytosine side, because of limits on close approach of the two Im rings and the geometry of sp2 hybridization about the amide nitrogen. CONCLUSIONS: Im and Py rings distinguish AT from GC base pairs because of steric factors involving the bulk of the guanine amine, and the ability of Im to form a hydrogen bond with the amine. Side-by-side Im and Py rings differentiate GC from CG base pairs because of tight steric contacts and sp2 hybridization at the amine nitrogen atom, with the favored conformations being G/Im,Py/C and C/Py,Im/G. Discrimination between AT and TA base pairs may be possible using bulkier rings, such as thiazole to select the A end of the base pair.

Photosensitization of human leukemic cells by anthracenedione antitumor agents.

1,4-Diamino-substituted anthraquinone antitumor agents (mitoxantrone and ametantrone) and structurally related 1,5- and 1,8-diamino-substituted compounds (AM1 and AM2) were tested for their ability to photosensitize human leukemic cells in culture. Viability was measured using the 3,4,5-dimethylthiazol-2,5-diphenyl tetrazolium bromide assay, and DNA and membrane damage were assessed. Following a 1-h exposure to AM2, a dose of drug required to give 50% loss of cell viability (53 microM) was obtained in the dark, which was reduced to approximately 2.4 microM following illumination for 2 min (lambda greater than 475 nm), a dose of light that was completely nontoxic to the cells in the absence of drug. A shift in the cell viability curve was also observed for AM1 but, under identical conditions, the dose modification was only 8.9. In contrast, neither ametantrone nor mitoxantrone gave a decreased viability upon illumination. DNA single-strand breaks as measured by alkaline elution correlated with cell viability. Frank DNA single-strand breaks were produced by AM2 and light, suggesting the production of free radicals. The strand breaks produced by AM2 in the dark and by mitoxantrone (with or without illumination) were protein concealed. No evidence of photo-induced membrane damage, as determined by transport of the model amino acid cycloleucine, could be observed even at supralethal doses.

Liblomycin-mediated DNA cleavage in human head and neck squamous carcinoma cells and purified DNA.

Liblomycin (LBM), a novel bleomycin analogue, and bleomycin A2 (BLM A2) were compared with respect to their relative potential to inhibit growth in a human head and neck squamous carcinoma cell line and to produce DNA damage within cellular DNA and nuclei DNA and against isolated naked DNA. Against the BLM-sensitive cell line 183A, the concentration of LBM that inhibits cell growth by 50% was 1.1 microM for a 30-min drug exposure, while it was 23 microM for BLM A2. Drug-mediated DNA double-strand cleavage within cells was compared with the relative ability of these drugs to produce DNA cleavage in isolated 183A cell nuclei. Though 30-min exposures of cells to equimolar concentrations of both drugs resulted in 4-fold greater cellular DNA damage by LBM than BLM A2, the two drugs were nearly equipotent in producing DNA injury within isolated nuclei. Against Simian virus 40 DNA, however, LBM was 10-fold less effective than BLM A2 in producing Forms II and III DNA from Form I DNA. Radioactivity from either [3H]BLM A2 or 125I-LBM found associated with cells after a 30-min incubation period was also assessed in the 183A cell line. The exposure of cells to radiolabeled drug (1 microM) resulted in a 71-fold greater amount of cell-associated radioactivity for LBM than for BLM A2. The relative abilities of the 183A cell line to partially reseal LBM- or BLM A2-mediated DNA double-strand breaks were also assessed. No preferential repair of overall drug-mediated DNA injury, however, was observed. Finally, drug-mediated specific cleavage sites on pBR322 DNA were determined. At doses that gave the same extent of DNA cleavage, both BLM A2 and LBM gave similar patterns of strand scission, although minor differences were observed. Taken together, these data demonstrate that the greater efficacy of LBM against the BLM-sensitive head and neck squamous cell line is due mainly to LBM's greater association with cells over a defined time period, even though the DNA cleaving ability of LBM is relatively lower than that of BLM A2.

Binding to DNA of selected lexitropsins and effects on prokaryotic topoisomerase activity.

The binding behaviour toward DNA of some minor groove binders related to distamycin was studied by means of circular dichroism. In addition their influence on the activity of topoisomerases isolated from Streptomyces noursei has been investigated. The monocationic imidazole containing ligands (lexitropsins) show a decreased affinity to AT pairs but an increased affinity to GC pairs which contrasts the AT-preferred binding of Dst-2 and Dst-3. For the monocationic triimidazole containing lexitropsin the affinity for GC over AT pairs was most pronounced. It was also found that the imidazole containing lexitropsins are inhibitors of topoisomerases. These minor groove binders interfere more strongly with the DNA gyrase activity than with the prokaryotic topoisomerase I. Our results indicate that Dst-3 most effectively inhibits gyrase and topoisomerase I activity. However, the inhibitory effect is neither related to the base pair specificity nor to the binding strength of different ligands. The mechanism of interference of minor groove binders with topoisomerase activity is more complex. It is considered that different factors, such as the nature of the ligand together with their DNA binding parameters and the target sequences of the enzymes play a role in the inhibitory effects of minor groove binders.

Variation of DNA sequence specificity of DNA-oligopeptide binding ligands related to netropsin: imidazole-containing lexitropsins.

CD binding studies of nonintercalative oligopeptides related to netropsin, named lexitropsins, have been carried out with synthetic duplex DNAs and natural DNA. While netropsin possesses a high dA.dT sequence specificity, these ligands show a progressive lowering of the ability to bind to dA.dT basepairs in DNA and a dramatic reduction of the sequence specificity seen at high salt concentration due to a replacement of pyrrole moieties by imidazoles. This variation in DNA sequence specificity of lexitropsins is mirrored in corresponding large differences in the template inactivation of poly(dA-dT).poly(dA-dT) in the RNA polymerase reaction by these drugs. The presence of imidazole permits binding of the oligopeptide to dG.dC pairs, which is most effective for the triimidazole peptide. Results at increasing salt concentration reveal, however, that a tight binding to pure dG.dC sequences does not occur. A proper sequence containing dG.dC and dA.dT pairs is supposed to be required for a higher specificity. The CD data accord well with previously reported melting studies and are in favor of recent theoretical results suggesting that the diminished AT preference may be due to an increase in the complexation energy with the dG.dC pairs.

Effects of analogs of the DNA minor groove binder Hoechst 33258 on topoisomerase II and I mediated activities.

By contrast with other DNA minor groove binders, Hoechst 33258 inhibited topoisomerase-mediated activity in intact cells. To determine whether specific structural alterations could modify the topoisomerase reactivity of this drug, a series of analogs of Hoechst 33258 (compound 1) was examined. When the relative DNA binding affinities (Ka) of these agents were determined, compound 1 had the highest Ka while agents with substitutions in either of the benzimidazole moieties showed reduced affinity. Whether these changes in DNA binding correlated with topoisomerase inhibitory potency was next examined. In isolated nuclei, 25 microM of agents 1, 5 and 7 reduced VM-26 induced cross-links by 64, 65 and 83%, compared with 15 to 25% reductions by agents 2, 3, 4 and 6, respectively. The structural modification common to the less active compounds was the substitution of an oxygen for nitrogen at either position 1 or 2. On the basis of these results, agents 1, 2, 3 and 7, representing a range of inhibitory potency, were chosen for further analyses. Cross-link induction by m-AMSA and camptothecin in isolated nuclei, as well as by VM-26 in intact cells, was inhibited to a greater extent by agents 1 and 7 than 2 or 3. Additionally, all four drugs inhibited relaxation of pBR 322 DNA induced by both topoisomerases, although topoisomerase I was 2 to 5-fold more sensitive than topoisomerase II. A linear correlation was observed between the logarithms of the Ka value of compounds 1, 2 and 3 and their IC25 values for both topoisomerases, suggesting a strong dependence on DNA binding affinity for enzyme inhibition. Nevertheless, agent 7, despite having less affinity for calf thymus DNA than 1, was the most potent topoisomerase inhibitor tested in intact cells and in isolated enzyme systems. Thus, retention of nitrogen at positions 1 and 2 as well as the addition of nitrogen at position 16 was associated with increased topoisomerase inhibitory potency.

Netropsin and bis-netropsin analogs as inhibitors of the catalytic activity of mammalian DNA topoisomerase II and topoisomerase cleavable complexes.

This study examined the ability of netropsin and related minor groove binders to interfere with the actions of DNA topoisomerases II and I. We evaluated a series of netropsin dimers linked with flexible aliphatic chains of different lengths. These agents are potentially able to occupy longer stretches of DNA than the parental drug as a result of bidentate binding. Both netropsin and its dimers were found: (i) to inhibit the catalytic activity of isolated topoisomerase II and (ii) to interfere with the stabilization of the cleavable complexes of topoisomerase II and I in nuclei. Dimers with linkers consisting of 0-4 and 6-9 methylene groups (n) were far more inhibitory than netropsin against isolated enzyme and in the nuclear system. The compound with n = 5 was less active than netropsin in both assays while the dimer with n = 10 inhibited only the isolated enzyme. The comparison of dimers with fixed linker length (n = 2) but varying number of N-methylpyrrole residues (from 1 to 3) revealed that the inhibitory properties were enhanced with increasing number of N-methylpyrrole units. For dimers with varying linker length, drug ability to inhibit catalytic activity of isolated topoisomerase II was positively correlated with calf thymus DNA association constants. In contrast, no such correlation existed in nuclei. However, the inhibitory effects in the nuclear system were correlated with the association constants for poly(dAdT). The results indicate that bidentate binding can significantly enhance anti-topoisomerase activity of netropsin related dimeric minor groove binders. However, other factors such as the length of the linker, the number of pyrrole moieties and the nature of the target (isolated enzyme/DNA versus chromatin in nuclei) also contribute to these activities.

Anthracycline and anthraquinone anticancer agents: current status and recent developments.

The clinical treatment of neoplastic diseases relies on the complementary procedures of surgery, radiation treatment, immunotherapy and chemotherapy. The latter technique has matured from its earliest applications of mustard alkylating agents in the 1940s to an increasingly rationally based discipline, which is contributing significantly to the management of human malignancies. As the field of chemotherapy matured, several promising natural anticancer agents were identified. However, a more urgent need soon arose from the common experience of clinically limiting toxicities of most anticancer drugs, i.e. the necessity to develop less toxic clinical drug candidates. Thus, the medicinal chemist turned towards analog development involving certain anthraquinones. Hand-in-hand with this considerable synthetic effort, which uncovered several promising clinical leads, biochemical pharmacology, or study of the mechanisms of action of clinical anticancer agents, afforded deeper insight into drug metabolism and mode of action. More recently, therefore, the field of synthetic organic chemistry, which has been complemented by the methods of microbial chemistry, has been faced with new synthetic challenges, occasioned by the identification of hitherto unrecognized cellular targets for anticancer drugs, such as topoisomerases and helicases. The armementarium of the oncologist currently includes about 40-50 clinically useful chemical agents. The paradigm of cytotoxic anticancer agents is doxorubicin, an anthracycline, which is still amongst the most widely prescribed and effective of anticancer agents. The review attempts to summarize the discovery of anthracyclines and the elucidation of their several mechanisms of action and efforts towards improvement of their therapeutic efficacy.

Phototherapeutic potential of alternative photosensitizers to porphyrins.

Because of promising clinical results obtained with photodynamic therapy, more and more photosensitizers continue to be isolated (from natural sources), synthesized and evaluated, the development of which is considered to be a key factor for the successful clinical application of photodynamic therapy. Porphyrins and their analogs (as classical types of phototherapeutic agents) have been extensively reviewed. In this review, we have attempted to summarize the phototherapeutic potential (in particular, anticancer and antiviral aspects) of nonporphyrin photosensitizers (as a new generation of phototherapeutic agents) in more detail, which have been relatively much less reviewed hitherto. They include anthraquinones, anthrapyrazoles, perylenequinones, xanthenes, cyanines, acridines, phenoxazines and phenothiazines. They have shown certain phototherapeutic advantages over the presently used porphyrins. Some anthraquinones, perylenequinones, cyanines, phenoxazines and phenothiazines exhibit strong light absorption in the 'phototherapeutic window' (600-1000 nm), high photosensitizing efficacy and low delayed skin photosensitivity. Some of the nonporphyrin photosensitizers (such as rhodamine 123, merocyanine 540 and some cyanine cationic dyes) demonstrate higher selectivity for tumor cells. They can also be explored in connection with selective carcinoma photolysis strategy based on mitochondrion-, lysosome- or DNA-directed localization mode.

Synthetic DNA minor groove-binding drugs.

In this review, both cationic and neutral synthetic ligands that bind in the minor groove of DNA are discussed. Certain bis-distamycins and related lexitropsins show activities against human immunodeficiency virus (HIV)-1 and HIV-2 at low nanomolar concentrations. DAPI binds strongly to AT-containing polymers and is located in the minor groove of DNA. DAPI intercalates in DNA sequences that do not contain at least three consecutive AT bp. Berenil can also exhibit intercalative, as well as minor groove binding, properties depending on sequence. Furan-containing analogues of berenil play an important role in their activities against Pneumocystis carinii and Cryptosporidium parvuam infections in vivo. Pt(II)-berenil conjugates show a good activity profile against HL60 and U-937 human leukemic cells. Pt-pentamidine shows higher antiproliferative activity against small cell lung, non-small cell lung, and melanoma cancer cell lines compared with many other tumor cell lines. trans-Butenamidine shows good anti-P. carinii activity in rats. Pentamidine is used against P. carinii pneumonia in individuals infected with HIV who are at high risk from this infection. A comparison of the cytotoxic potencies of adozelesin, bizelesin, carzelesin, cisplatin, and doxorubicin indicates that adozelesin is a potent analog of CC-1065. Naturally occurring pyrrolo[2,1-c][l,4]benzodiazepines such as anthramycin have a 2- to 3-bp sequence specificity, but a synthetic PBD dimer spans 6 bp, actively recognizing a central 5'-GATC sequence. The crosslinking efficiency of PBD dimers is much greater than that of other major groove crosslinkers, such as cisplatin, melphalan, etc. Neothramycin is used clinically for the treatment of superficial carcinoma of the bladder.

Rational recognition of nucleic acid sequences.

Recent progress in synthetic and computational chemistry has made it possible to develop certain novel drug candidates. Drug candidates for genetic diseases, such as cancer, may also be designed on the basis of structural information obtained using X-ray analysis and NMR, as well as evidence from biological techniques applied to natural products - DNA (or RNA) complexes and conjugates. The resulting designed drug candidates exhibit promising performance based on the recognition on nucleic acid sequences.

Hybrid molecules containing propargylic sulfones and DNA minor groove-binding lexitropsins: synthesis, sequence specificity of reaction with DNA and biological evaluation.

A series of hybrids, 4-13, incorporating propargylic sulfones and minor groove-binding oligopeptide carriers, was synthesized. The anticipated preferential binding at adenine sites within the minor groove was confirmed by sequencing determination of these agents on high-resolution gels, indicating preferential alkylation at guanine, and significantly, high selectivity for 5'-GACG and 5'-GGTG. The ability of these hybrids to cleave DNA, as determined by agarose-gel assay, is consistent with the ethidium bromide fluorescence assay. The cytotoxicities of these compounds were also determined against human KB cells in vitro. Higher cytotoxic activities were observed for the compounds containing fewer N-methylpyrrole units, an imidazole group and a 2,3-disubstituted naphthyl moiety.

Photosensitization with anticancer agents. 20--EPR studies on the photodynamic action of phleichrome: formation of semiquinone radical and activated oxygen species on illumination with visible light.

When phleichrome was illuminated with visible light, the semiquinone radical, singlet oxygen, and superoxide anion radical were detected. The formation of the semiquinone radical and activated oxygen species and the transformations and competitions between them depend on quinone and oxygen concentration, duration and intensity of illumination, and the nature of the substrate. In anaerobic solution, the semiquinone radical was predominantly photoproduced via the self-electron transfer between the excited and ground species. In contrast, in aerobic solution, singlet oxygen is the principal product in the photosensitization of phleichrome. In addition to singlet oxygen, superoxide anion radical is also generated by the quinones upon illumination in aerobic solution, but to a lesser extent. The generation of the superoxide anion is significantly enhanced by the presence of electron donors.

Photosensitization with anticancer agents. 17. EPR studies of photodynamic action of hypericin: formation of semiquinone radical and activated oxygen species on illumination.

When hypericin was illuminated with 580 nm light in aqueous solution, the semiquinone radical, singlet oxygen, and superoxide anion radical were detected. The formation of the semiquinone radical and activated oxygen species and the transformation and competition between them depend on the quinone and oxygen concentrations, irradiation time and intensity, and the nature of substrate. In anaerobic solution containing a high concentration of the quinone, the semiquinone radical was predominantly photoproduced. In contrast, in aerobic solution, singlet oxygen is the principal product in the photosensitization of hypericin. Besides singlet oxygen, superoxide anion radical is generated by the quinone on illumination in aerobic solution via the reduction of oxygen by the semiquinone radical, but to a lesser extent than singlet oxygen. The generation of superoxide anion radical is significantly enhanced by the presence of electron donors.

Photosensitization with anticancer agents 19. EPR studies of photodynamic action of calphostin C: formation of semiquinone radical and activated oxygen on illumination with visible light.

When calphostin C was illuminated with visible light, the semiquinone radical, singlet oxygen, and superoxide anion radical were detected. The formation of the semiquinone radical and activated oxygen species and the transformations and competitions between them depend upon the quinone and oxygen concentrations, time and intensity of illumination, and the nature of the substrate. In anaerobic solution, the semiquinone radical was predominantly photoproduced via the self-electron transfer between the excited and ground species. In aerobic solution, singlet oxygen is the principal product in the photosensitization of calphostin C. In addition to singlet oxygen, superoxide anion radical is also generated by the quinones upon illumination in aerobic solution, but to a lesser extent than singlet oxygen. The superoxide anion is produced via the reduction of oxygen by the semiquinone radical, and this process is significantly enhanced by the presence of electron donors.

Photosensitization by antitumor agents, 4. Anthrapyrazole-photosensitized formation of single strand-breaks in DNA.

Single-strand breaks can be introduced into PM2 closed-circular DNA upon illumination with blue light, in the presence of the anthrapyrazole antitumor agent, compound 1. Damage is observed already after 1 min of blue light illumination, and is significantly enhanced by the presence of electron donors such as NADH, ascorbic acid or Fe(III)/EDTA complex. The photosensitizing properties were not observed for anthrapyrazole analogues with one or more hydroxyl substituents in the chromophore of the drug. The inhibitory effects of sodium azide, methanol, mannitol, SOD, and catalase suggest an oxygen-dependent mechanism of strand-break production, probably involving hydroxyl radicals. However, a second mechanism involving drug molecules bound to the DNA is also indicated under anoxic conditions in the presence of NADH.

Enzymatic oxidative activation and transformation of the antitumor agent mitoxantrone.

Ambient temperature incubation of the anticancer agent mitoxantrone with horseradish peroxidase and hydrogen peroxide converts it into a hexahydronaphtho[2,3-f]quinoxaline-7,12-dione in which one side chain has cyclized to the chromophore. The structure of this cyclic metabolite was secured by independent synthesis. This peroxidative conversion of mitoxantrone, the progress of which can be followed spectrophotometrically, is accompanied by formation of a free radical species. The EPR characteristics, and dependence on pH of the latter, suggest it exists as a radical cation. The enzymatic oxidation of mitoxantrone is totally irreversible. The purified cyclic metabolite is a substrate for the peroxidase affording the unstable fully oxidized diimino compound and this reaction is fully reversible upon addition of ascorbate or other biological reductants. Admixture of the fully oxidized diimino product with the reduced cyclic metabolite generates the corresponding radical cation species by disproportionation-comproportionation processes. Independent kinetic studies confirm that reaction of the peroxidase with the cyclic metabolite proceeds more rapidly than with mitoxantrone itself. A derivative of mitoxantrone, in which the side-chain secondary amine functions are acylated, generates a radical cation upon treatment with the peroxidase-H2O2 system but does not cyclize subsequently. Derivatives without phenolic hydroxyls or those in which the phenolic hydroxyls are blocked also undergo peroxidative reaction. These observations suggest that initial peroxidative attack occurs at the aromatic nitrogens of mitoxantrone. The possible relevance of these results to the anticancer action of mitoxantrone and the implications for suppression of lipid peroxidation in vivo are discussed.

Photosensitization by antitumor agents. 5. Daunorubicin-photosensitized oxidation of NAD(P)H in aqueous and N,N-dimethylformamide/aqueous solutions--an electron paramagnetic resonance study.

An EPR spectrum of the semiquinone radical of daunorubicin (D) was recorded upon illumination (480 nm) of the drug and NAD(P)H in deaerated aqueous and DMF/aqueous solutions. In the latter solvent system, an EPR spectrum with hyperfine structure was recorded. The kinetics of the photoinduced generation and decrease of the EPR signal intensity in the dark were measured. Second order rate constants for the radical recombination were derived for the two solvent systems. Photosensitized production of the superoxide radical, upon illumination of daunorubicin and NAD(P)H, in aerated aqueous or DMF/aqueous solutions, is evidenced by employing a spin trap DMPO (5,5-dimethyl-1-pyrroline-N-oxide) and an SOD assay. 5-Iminodaunorubicin (5-ID), in contrast to the parent compound (D), does not possess photosensitizing properties.

Minor-groove binders are inhibitors of the catalytic activity of DNA gyrases.

Non-intercalating DNA minor-groove binders may effectively inhibit the supercoiling activity of gyrases by influencing the enzyme recognition and cleavage site on DNA. For gyrase from Streptomyces noursei a wide range of inhibitory potency for different classes of ligands is observed. This can be explained by a number of structural and binding factors of the ligands competing with the gyrase on the target site of DNA, the mechanism of which is different from the classical gyrase inhibitors.

Studies on the ability of minor groove binders to induce supercoiling in DNA.

The effect of various non-intercalating minor groove binders on closed circular DNA in the presence of topoisomerase I has been studied by means of agarose gel electrophoresis. Analogues of the netropsin series (lexitropsins) and SN-6999 effectively produce positive supercoils, as indicated by analysis of the topoisomers in the presence of chloroquine and the evaluated linking number changes. Analogues of the distamycin series are less effective, and bisquaternary heterocycles, as well as DAPI and pentamidine, were found to be ineffective ligands. The large differences observed in the ability of minor groove binders to induce positive supercoils are discussed.