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The synthesis of a new pyridine analogue of netropsin, N,N'-bis[6-(N-3-dimethylaminopropyl) carbamoylpyridin-2-yl] pyridine-2,5-dicarboxamide (VII) is described. The potential for use of VII as a carrier to place chemical functionalities into the minor groove of DNA which are capable of modifying DNA is discussed.
The interaction of the antibiotics distamycin A, distamycin analogue and netropsin with chromatin of calf thymus has been studied by circular dichroism measurements and by gel filtration. The minor groove of DNA in chromatin is accessible by 83-89% to the binding of these antibiotics as compared with that of free DNA. The present results combined with our data on the methylation of chromatin with dimethylsulphate [3] strongly suggest that the minor groove of DNA in chromatin is not occupied by chromatin proteins.
ORD measurements of nucleic acids in the presence of the oligopeptides netropsin and distamycin A have indicated association of the antibiotics with DNA and strong conformational changes of the DNA structure with specificity to AT-rich helical regions. The RNA conformation is relatively unaffected by these antibiotics. The results are explained in terms of a perturbation of the DNA secondary structure as well as of the chromophore system of the oligopeptides.
The small basic oligopeptide antibiotic, netropsin, can be successfully employed as an effective counterselecting agent in Saccharomyces cerevisiae. The use of the drug results in approximately a 35-fold enrichment of auxotrophic mutants in a mutagenized culture of yeast. The experimental procedure is quite simple and less time consuming than other presently used methods for indirect mutant selection in yeast.
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Control of gene expression is a cherished goal of cancer chemotherapy. Small ligand molecules able to bind tightly to DNA in a well-defined configuration are being actively searched for. With this goal in mind, we have designed and synthesized the trifunctional molecule R-132, which combines a bispyrrole skeleton for minor groove DNA recognition and two different chromophores, anilinoacridine and ethidium. The affinity and mode of binding of R-132 to DNA were studied by a combination of complementary biochemical and biophysical techniques, which included absorption and fluorescence spectroscopy and circular and linear dichroism. A surface plasmon resonance biosensor analysis was also performed to quantify the kinetic parameters of the drug-DNA interaction process. Altogether, the results demonstrate that the three moieties of the hybrid molecule are engaged in the interaction process, thus validating the rational design strategy. At the biological level, R-132 stabilizes topoisomerase-II-DNA covalent complexes and displays potent cytotoxic activities, which are attributable to its DNA-binding properties. R-132 easily enters and accumulates in cell nuclei, as evidenced by confocal microscopy. R-132 therefore provides a novel lead compound for the design of gene-targeted anticancer agents.
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We report the synthesis, DNA-binding properties and antitumor activity of ThiaNetGA, a hybrid molecule in which are conjugated a thiazole-lexitropsin and an intercalating anilinoacridine chromophore. This combilexin molecule binds to DNA via a bimodal process involving minor groove binding of the lexitropsin moiety and intercalation of the acridine moiety. The uptake and distribution of the hybrid in L1210 leukemia cells were investigated by ESR spectroscopy using a spin-labeled derivative. The nitroxide-containing conjugate accumulates preferentially in the cell nuclei and rapidly saturates the nuclear receptor sites. Both in vitro and in vivo assays indicate that the drug is practically nontoxic but exhibits moderate antitumor activity against P388 leukemia cells in mice.
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NMR spectroscopy combined with molecular modeling was used to characterize a heterodimeric complex with Dst and 2-ImN bound in the minor groove of d(GCCTAACAAGG).d(CCTTGTTAGGC) (1:1:1 2-ImN.Dst.DNA complex). The imidazole-pyrrole-pyrrole ligand 2-ImN spans 5'-GTTA-3' of the TAACA.TGTTA binding site with the imidazole nitrogen specifically recognizing the guanine amino group. The Dst ligand lies along the 5'-AACA-3' sequence and complements the 2-ImN ligand in the formation of the antiparallel side-by-side heterodimeric complex. Titrations of the same site with Dst or 2-ImN alone yield homodimeric complexes (2:1 ligand.DNA) of lower stability than the 1:1:1 2-ImN.Dst.DNA complex. Dst and 2-ImN binding to d(CGCAAACTGGC).d(GCCAGTTTGCG) was also investigated. The 1:1:1 2-ImN.Dst.DNA complex is again the most stable complex with the AAACT.AGTTT site and is similar to the TAACA.TGTTA complex. No monomeric binding of either 2-ImN or Dst was observed to either site.
he synthesis, DNA binding and in vitro photoinduced cytotoxic properties of a number of minor groove and sequence-directed psoralen and coumarin conjugates of pyrrole- and imidazole-containing distamycin analogues 2-5 are described. Results from an ethidium displacement assay on calf thymus and T4 DNA suggest that like distamycin these agents bind strongly to the minor groove of DNA. The data show that these conjugates exhibit a lower AT preference than distamycin and the decrease is significantly greater for the imidazole-containing compounds. All of the compounds along with 8-methoxypsoralen, 1, were relatively noncytotoxic in the dark with only the imidazole-psoralen compound 3 giving an IC50 value below 100 microM. Following UV activation, all compounds showed an increased potency with photoinduced dose modifications in the human chronic myeloid leukemia K562 cells of > 333, 12, > 1.3, and > 2.5 for compounds 2-5, respectively, under the UV irradiation conditions employed. The psoralen-pyrrole analogue 2 was over 300 times more active following UV activation than agent 1, 250 times more potent than the corresponding coumarin conjugate 4, and 15-fold more potent than its imidazole analogue 3. Data from CD dilution (with DMF) studies show that upon irradiation with light at 366 nm, compounds 2-5 bind irreversibly to DNA. Furthermore, upon irradiation compound 2 produced interstrand cross-linked DNA in quantitative yield, with isolated DNA, at > 300- and > 3000-fold lower drug concentrations than the imidazole analogue 3 and 8-methoxypsoralen, respectively. As expected coumarin conjugates 4 and 5 did not produce any cross-linked DNA under any conditions. Since the psoralen conjugates are more phototoxic than their coumarin analogues, these results suggest that DNA interstrand cross-link formation may be an important mechanism by which they exert their biological activity in cells. In addition, the enhanced photocytotoxic potency of conjugate 2 over 3 may be related to its larger binding constant, more efficient DNA cross-linking ability, and possibly to its preference for AT-rich sequences.