5616-82-0Relevant academic research and scientific papers
Toward the design of an RNA:DNA hybrid binding agent
Chu, Wenhua,Kamitori, Shigehiro,Shinomiya, Miho,Carlson, Robert G.,Takusagawa, Fusao
, p. 2243 - 2253 (2007/10/02)
One characteristic function of the retroviruses, which is generally not found in normal eukaryotic cells, is production of a long RNA:DNA hybrid in the viral replication phase. If agents are designed which bind only to the RNA:DNA hybrid, but neither to DNA nor to RNA, such agents will be able to inhibit specifically the RNase H activity of retroviral reverse transcriptase, and therefore will suppress viral replication. Actinomycin D binds to double-stranded DNA, but not to RNA, because steric hindrance between the 2-amino group of the phenoxazinone ring and the 2'-hydroxyl group of RNA prevents intercalation of the antibiotic. However, if the C8-H in the phenoxazinone ring is replaced by an aromatic nitrogen N8, a strong hydrogen bond acceptor, this analog (N8-actinomycin D) might be able to bind intercalatively to an RNA:DNA hybrid by forming an additional hydrogen bond between N8 and the 2'-hydroxyl group of guanosine ribose. This hypothesis has been tested by a molecular mechanics calculation using a model structure of the complex between N8-actinomycin D and a small RNA:DNA hybrid, r(GC):d(GC). The results of the molecular mechanics calculation suggest that N8-actinomycin D can intercalatively bind to the RNA:DNA hybrid by making an additional intracomplex hydrogen bond. This hydrogen bonding capability of N8 has been confirmed in the crystal structure of the chromophore of N8-actinomycin D. Thus, N8-actinomycin D has been synthesized by coupling the pyridine and benzene fragments obtained independently. A binding study indicates that both actinomycin D and N8-actinomycin D bind intercalatively not only to DNA:DNA double strands but also to RNA:DNA hybrids. Although the overall binding capacity of N8-actinomycin D is reduced substantially in comparison with that of actinomycin D itself, N8-actinomycin D tends to bind relatively more favorably than actinomycin D to the RNA:DNA hybrids. Thus, this initial attempt at designing an RNA:DNA hybrid binding agent appears to be successful. However, it is necessary to modify the agent further to increase its RNA:DNA hybrid binding character and to decrease the DNA:DNA binding character, in order to make a useful RNA:DNA hybrid binding agent.
Role of D-valine residues in the antitumor drug actinomycin D: Replacement of D-valines with other D-amino acids changes the DNA binding characteristics and transcription inhibitory activities
Chu, Wenhua,Shinomiya, Miho,Kamitori, Kazuyo Y.,Kamitori, Shigehiro,Carlson, Robert G.,Weaver, Robert F.,Takusagawa, Fusao
, p. 7971 - 7982 (2007/10/02)
D-valine analogues of the antitumor drug actinomycin D, in which D-valine residues were replaced with D-threonine, D-tyrosine, D-phenylalanine, and D-O-methyltyrosine residues, have been totally synthesized. The crystal structure of the D-O-methyltyrosine analogue has been determined (a = b = 21.352(6), c = 44.525(9) ?; space group P41212; R = 0.19 for 803 out of 1114 reflections at 1.8 ? resolution data). Replacements of D-valines did not change the overall conformation of the molecule, and the substituted groups were located on the side opposite to the DNA binding site, suggesting that the analogues can bind intercalatively at 5'-GC-3' sequences of DNA like actinomycin D does. In the crystals, the analogue molecules constitute a tight dimer, and a pair of stacked chromophores of the dimer was further sandwiched by two methoxyphenyl groups of neighboring molecules. These strong aromatic aromatic stacking forces among the molecules appear to reduce very much the water solubility of the aromatic analogues. The characteristics of binding of the analogues to various DNA's including d(GAAGCTTC)2, d(GTTGCAAC)2, poly(dA-dT), poly(dG-dC), and calf thymus DNA have been examined by using the visible spectrum methods. Difference spectra of actinomycin D and the analogues with oligonucleotides indicated that the analogues bind intercalatively to the DNA, as actinomycin D does, but the association constants were reduced to approximately one-half that of actinomycin D. The spectra of the aromatic analogues titrated with calf thymus DNA indicated that the aromatic analogues bound somehow differently to the longer DNA's. A simple profile analysis of the spectra suggested that the aromatic analogues bound to calf thymus DNA not only with intercalation, as actinomycin D does, but also with side binding. Nevertheless, the association constants of the aromatic analogues to calf thymus DNA with the intercalation mode were found to be quite similar to those of the short oligonucleotides. This conclusion has been supported by the melting behaviors of the DNA with the aromatic analogues, in which the melting curves of the analogues were superimposable on the melting curve of DNA with actinomycin D, suggesting that the aromatic analogue molecules were intercalated into the DNA. The inhibitory activities of actinomycin D and analogues on RNA polymerase in vitro were examined using calf thymus DNA and E. coli RNA polymerase. All actinomycin D analogues severely inhibited RNA synthesis at relatively low drug concentrations. In general, inhibitory activities of the analogues on the RNA synthesis were found to be correlated with those of DNA binding characteristics. However, the analogue in which D-phenylalanine replaced D-valines inhibited RNA synthesis more strongly than actinomycin D itself, but this analogue bound to the DNA's much more weakly than actinomycin D. In this study, the D-valine residues in the cyclic depsipeptides of actinomycin D were found not to be directly involved in DNA binding, but this amino acid residue was found to be an important biological medulator of the antibiotic. Although the D-valine is a hydrophobic amino acid residue, this amino acid residue appears to play an important role in increasing the water solubility of the antibiotic. Replacements of D-valine residues reduced drastically the water solubility of the analogues, and consequently, this physical character of the analogues reduced their capacities for binding to DNA. As a result, the biological activities of the analogues were generally decreased.
