Identification Of Substituents Research Articles

Topoisomerase II−Drug Interaction Domains: Identification of Substituents on Etoposide That Interact with the Enzyme

Etoposide is one of the most successful chemotherapeutic agents used for the treatment of human cancers. The drug kills cells by inhibiting the ability of topoisomerase II to ligate nucleic acids that it cleaves during the double-stranded DNA passage reaction. Etoposide is composed of a polycyclic ring system (rings A-D), a glycosidic moiety at the C4 position, and a pendent ring (E-ring) at the C1 position. Although drug-enzyme contacts, as opposed to drug-DNA interactions, mediate the entry of etoposide into the topoisomerase II-drug-DNA complex, the substituents on etoposide that interact with the enzyme have not been identified. Therefore, saturation transfer difference [1H]-nuclear magnetic resonance spectroscopy and protein-drug competition binding assays were employed to define the groups on etoposide that associate with yeast topoisomerase II and human topoisomerase IIalpha. Results indicate that the geminal protons of the A-ring, the H5 and H8 protons of the B-ring, and the H2' and H6' protons and the 3'- and 5'-methoxyl protons of the pendent E-ring interact with both enzymes in the binary protein-ligand complexes. In contrast, no significant nuclear Overhauser enhancement signals arising from the C-ring, the D-ring, or the C4 glycosidic moiety were observed with either enzyme, suggesting that there is limited or no contact between these portions of etoposide and topoisomerase II in the binary complex. The functional importance of E-ring substituents was confirmed by topoisomerase II-mediated DNA cleavage assays.

Location and identification of substituents with free amino group in lipopolysaccharides of Gram-negative bacteria with the use of chromophore labelling

Interaction of ten different lipopolysaccharides (LPS) with 2,4-dinitrofluorobenzene yielded quantitatively yellow dinitrophenyl derivatives (DNP-LPS) to show the presence of substituents with free amino group. The DNP-LPS samples were degraded with 1% acetic acid, and after removal of lipid A precipitates the supernatants were separated on a Sephadex G-25 column to give coloured polysaccharide, oligosaccharide and monomeric fractions monitored at lambda DNP = 365 nm. The coloured materials, including DNP-derivative of lipid A, were dephosphorylated with hydrofluoric acid followed by identification of the released DNP-amines by thin layer chromatography (TLC) on silica gel. Subsequently, the dephosphorylated materials were hydrolysed with hydrochloric acid followed by TLC analysis. The approach allowed to detect, locate and identify the substituents with free amino group within the LPS molecules. Moreover, two types of core structures within LPS preparation from one strain were discovered for five microorganisms.

Location and identification of substituents with free amino group in lipopolysaccharides of Gram-negative bacteria with the use of chromophore labelling

Interaction of ten different lipopolysaccharides (LPS) with 2,4-dinitrofluorobenzene yielded quantitatively yellow dinitrophenyl derivatives (DNP-LPS) to show the presence of substituents with free amino group. The DNP-LPS samples were degraded with 1% acetic acid, and after removal of lipid A precipitates the supernatants were separated on a Sephadex G-25 column to give coloured polysaccharide, oligosaccharide and monomeric fractions monitored at lambda DNP = 365 nm. The coloured materials, including DNP-derivative of lipid A, were dephosphorylated with hydrofluoric acid followed by identification of the released DNP-amines by thin layer chromatography (TLC) on silica gel. Subsequently, the dephosphorylated materials were hydrolysed with hydrochloric acid followed by TLC analysis. The approach allowed to detect, locate and identify the substituents with free amino group within the LPS molecules. Moreover, two types of core structures within LPS preparation from one strain were discovered for five microorganisms.

Proposed structure for the noncovalently associated heme prosthetic group of dissimilatory nitrite reductases. Identification of substituents.

The substituents of the noncovalently associated heme prosthetic group of the bacterial nitrite reductase-cytochrome oxidase (EC 1.9.6.1 or EC 1.9.3.2.) from Pseudomonas aeruginosa (ATCC 19429) and Paracoccus denitrificans (ATCC 13456) have been identified. This was accomplished by 1H NMR, infrared, visible, and mass spectroscopic techniques applied to semi-purified heme and purified methyl ester derivatives of the iron-free porphyrin. The main structural features are as follows. 1) The macrocycle is a reduced porphyrin of the chlorin type, that is, one of the pyrrole rings has been saturated so that the beta-carbons have sp3-hybridization. 2) The chlorin is a tetracarboxylic acid. 3) The substituents of the saturated pyrrole ring are two methyl groups and two hydroxymethyl groups. 4) The substituents of the unsaturated pyrrole rings are: (i) two methyl groups (ii) a propionic acid (iii) an acrylic acid, and (iv) two directly bonded formic acid groups. No firm evidence has been obtained for the relative positions of these unsaturated beta-pyrrolic substituents around the macrocyclic ring, but a proposed structure will be discussed. Several previously inexplicable chemical properties of the heme in extracts or in the intact enzyme can be now interpreted in view of the proposed structure. The trivial name "acrylochlorin" is suggested for the macrocycle.