Synthesis,DNA binding and topoisomerase inhibition of mononaphthalimide homospermidine derivatives

Two novel mononaphthalimide homospermidine derivatives （2a, 2b） with three or four methylene unit as linkages were synthesized and evaluated for cytotoxicity against human leukemia K562, murine melanoma B 16 and Chinese hamster ovary CHO cell lines. The presence of homospermidine motif could greatly elevate the potency of 1,8-naphthalimide. Conjugate 2b with longer spacer exhibited higher in vitro cytotoxicity than 2a. The DNA binding experiments indicated that conjugates 2b could bind to herring sperm DNA. The topoisomerase Ⅱ poison trials revealed that 2b could inhibit the activity of top. Ⅱ.     

Topology effect for DNA structure of cisplatin: topological transformation of cisplatin-closed circular DNA adducts by DNA topoisomerase I.

The reaction of cis-Pt(NH3)2Cl2(cis-DDP)-closed circular DNA adducts with DNA topoisomerse I(topo I) were studied by electron microscopy. We identified unique topoisomers such as a singly-linked catenane (2(1)2), trefoil (3(1), and dimetric catenane (2(1)2), etc., by analysis with electron micrographs. These unique recombination products resulted from cis-DDP-intra-twisting looped DNA adducts by DNA topo I, and the products could be explained a new mechanism based on an odd-even number rule. Our results suggest a new model on the working mechanisms for DNA topology of cis-DDP which enhances the recombination of DNA. Based on our results, we propose the topological idea that the yields of a mini closed circular DNA and pseudo trefoil DNA, etc., can be expected by reaction of cis-DDP-DNA-histone complexes with DNA topo I in the body.     

Pyrrolic tripodal receptors for carbohydrates. Role of functional groups and binding geometry on carbohydrate recognition

The contribution from several H-bonding groups and the impact of geometric requirements on the binding ability of benzene-based tripodal receptors toward carbohydrates have been investigated by measuring the affinity of a set of structures toward octyl β-D-glucopyranoside, selected as a representative monosaccharide. The results reported in the present study demonstrate that a judicious choice of correct geometry and appropriate functional groups is critical to achieve the complementary hydrogen bonding interactions required for an effective carbohydrate recognition.     

Computation of the contribution from the cavity effect to protein-ligand binding free energy

We present results of the investigation of the cavity creation/annihilation effect in view of formation of the protein-ligand (PL) complexes. The protein and ligand were considered as rigid structures. The change of the cavity creation/annihilation free energy DeltaG(cav) was calculated for three PL complexes using the thermodynamic integration procedure with the original algorithm for growing the interaction potential between the cavity and the water molecules. The thermodynamic cycle consists of two stages, annihilation of the cavity of the ligand for the unbound state and its creation at the active site of the protein (bound state). It was revealed that for all complexes under investigation, the values of DeltaG(cav) are negative and favorable for binding. The main contribution to DeltaG(cav) appears due to the annihilation of the cavity of the ligand. All computations were made using the parallel version of CAVE code, elaborated in our preceding work.     

The role of the Zn(II) binding domain in the mechanism of E. coli DNA topoisomerase I

Background  

Escherichia coli DNA topoisomerase I binds three Zn(II) with three tetracysteine motifs which, together with the 14 kDa C-terminal region, form a 30 kDa DNA binding domain (ZD domain). The 67 kDa N-terminal domain (Top67) has the active site tyrosine for DNA cleavage but cannot relax negatively supercoiled DNA. We analyzed the role of the ZD domain in the enzyme mechanism.     

Temperature effects on positronium formation and inhibition: a contribution to the elucidation of early spur processes. I. Glycerol/water mixtures

In order to elucidate the mechanism of positronium (Ps) formation in liquids, the effect of temperature, T, on the inhibiting properties of various solutes has been investigated in glycerol/water mixtures. Whereas the inhibition constants of Cl^? and I^? are found to increase markedly with T, that of CH₃NO₂ is T insensitive and that of NO₃^? diminishes with T. These findings are consistent with our previous model, according to which Ps would be formed via two pathways, either through the quasi-free entities or by the reaction of localized, not yet fully solvated, electrons and positrons. The increase with T of the Ps yield is found to be due to the fraction arising from the latter reaction. The results confirm Cl^? and I^? react with e_loc⁺, while CH₃NO₂ and NO₃^? scavenge quasi-free electrons. Regarding the behaviour of the inhibition constants of these latter solutes, a provisional explanation is given: CH₃NO₂ would scavenge epithermal electrons while NO₃^? would react with electrons at a lower energy state, in competition with the localization process. Hot Ps atoms are not likely to be involved.     

Effect of E-ring modifications in camptothecin on topoisomerase I inhibition: a quantum mechanics treatment

Camptothecins (CPTs) are the prototypical class of topoisomerase I (Top1) inhibitors with significant anticancer activities. Structure-activity relationship studies have demonstrated that inverting the stereochemistry at C-20 (R-CPT) or changing the E-ring lactone to a lactam (CPT-lactam) abolishes the Top1 inhibitory activity. The explanations that have been advanced for these effects are that there is either a failure of hydrogen bond formation involving the C-20 hydroxyl group of R-CPT or a failure of E-ring opening of the lactam, which have been proposed to be required for Top1 inhibition. We demonstrate here that the preferred conformation for the CPTs has the 20-Et pseudoaxial, while the 20-OH is pseudoequatorial, and therefore, the 20-OH groups in all the three CPT analogues (S-CPT, R-CPT, and CPT-lactam) are able to hydrogen bond with Asp533. The loss of the Top1 inhibitory activity by the latter two CPT analogues is attributed to the decreased pi-pi stacking interaction energy with the neighboring base pairs compared to the natural S-CPT. The differences in pi-pi stacking interaction energies are derived from the differential electrostatics on the E-ring.     

Accessibility of the carbohydrate moiety of membrane-boound rhodopsin to enzymatic and chemical modification

Galactose was specifically inserted into the carbohydrate moiety of rhodopsin by incubating retinal disk membranes with UDP-galactose: N-acetylglucosamine galactosyltransferase. The stoichiometry of labeling ranged from 1.2 to 1.8 (average = 1.5) residues of galactose per molecule of rhodopsin, indicating that some or all of the oligosaccharide chains of membrane-bound rhodopsin are readily accessible to enzymatic modification. These modified membranes were treated with galactose oxidase to generate an aldehyde at the C-6 position of the inserted galactose units. The enzymatically-oxidized membranes were then reacted with dansyl hydrazide to yield a fluorescent hydrazone which is sufficiently stable to permit spectroscopic analysis. This procedure for the specific attachment of a spectroscopic probe should be applicable to a wide variety of membrane glycoproteins.     

Evaluating the enthalpic contribution to ligand binding using QM calculations: effect of methodology on geometries and interaction energies

As a result of research on ligand efficiency in the pharmaceutical industry, there is greater focus on optimizing the strength of polar interactions within receptors, so that the contribution of overall size and lipophilicity to binding can be decreased. A number of quantum mechanical (QM) methods involving simple probes are available to assess the H-bonding potential of different heterocycles or functional groups. However, in most receptors, multiple features are present, and these have distinct directionality, meaning very minimalist models may not be so ideal to describe the interactions. We describe how the use of gas phase QM models of kinase protein-ligand complex, which can more closely mimic the polar features of the active site region, can prove useful in assessing alterations to a core template, or different substituents. We investigate some practical issues surrounding the use of QM cluster models in structure based design (SBD). These include the choice of the method; semi-empirical, density functional theory or ab-initio, the choice of the basis set, whether to include implicit or explicit solvation, whether BSSE should be included, etc. We find a combination of the M06-2X method and the 6-31G* basis set is sufficiently rapid, and accurate, for the computation of structural and energetic parameters for this system.     

Fragmentation of carbohydrate anomeric alkoxy radicals. synthesis of polyhydroxy piperidines and pyrrolidines related to carbohydrates

Imino sugars of the piperidine and pyrrolidine types can be specifically obtained when protected 5-amino-5-deoxyfuranopentoses, 5-amino-5-deoxyfuranohexoses, 6-amino-6-deoxyfuranohexoses, and 6-amino-6-deoxypyranohexoses undergo a tandem alkoxy radical beta-fragmentation-intramolecular cyclization reaction. The reaction is promoted by the system: iodosylbenzene-iodine under mild conditions. The tert-butoxycarbonyl, benzyloxycarbonyl, and diphenylphosphinoyl radicals have been studied as amino-protecting groups. Using this methodology, polyhydroxylated pyrrolidines of the D-erythrofuranoses 34 and 35, D-threofuranose 36, L-xylofuranose 42, and D-arabinofuranose 43 series and polyhydroxylated piperidines of the D-arabinopyranose type 37 and 38 were obtained.     

Allium carbohydrates I. Isolation and characterization of the polysaccharides

Summary 1. The amounts of glucofructans in 15 species of plants of the genusAllium L. growing in Central Asia have been studied.2. The polydispersity of all the glucofructans isolated has been established. Fractionation of the glucofructan fromA. sativum L. yielded homogeneous fractions with mol. wt. 1900 and 5000. On the basis of their IR spectra and the results of periodate oxidation, they have been assigned to the glucofructans of the inulin type.Institute of the Chemistry of Plant Substances, Academy of Sciences of the Uzbek SSR, Tashkent. Translated from Khimiya Prirodnykh Soedinenii, No. 2, pp. 137–142, March–April, 1979.     

Analysis of DNA relaxation and cleavage activities of recombinant Mycobacterium tuberculosis DNA topoisomerase I from a new expression and purification protocol

Background  

Mycobacterium tuberculosis DNA topoisomerase I is an attractive target for discovery of novel TB drugs that act by enhancing the accumulation of the topoisomerase-DNA cleavage product. It shares a common transesterification domain with other type IA DNA topoisomerases. There is, however, no homology between the C-terminal DNA binding domains of Escherichia coli and M. tuberculosis DNA topoisomerase I proteins.     

The effect of DNA binding on initial 8-methoxypsoralen photochemistry.

Abstract—Flash photolysis experiments on the complex of 8-methoxypsoralen with calf thymus DNA have shown binding promotes the anaerobic quenching of the 8-MOP triplet state and inhibits the accessibility to oxygen. The results indicate dark psoralen-DNA interactions suppress the singlet oxygen generation observed in prior work.     

Antitumor agents. I. DNA topoisomerase II inhibitory activity and the structural relationship of podophyllotoxin derivatives as antitumor agents.

Various podophyllotoxin derivatives from desoxypodophyllotoxin (DPT) were synthesized to examine the structural relationships between the biological significance (cytotoxic effect, effects on DNA topoisomerase II and tubulin polymerization) in vitro and antitumor activity in vivo (L 1210). An intact 6,7-methylenedioxy group of DPT is necessary to inhibit tubulin polymerization and topoisomerase II. 4'-Phenolic hydroxyl group of DPT is essential to inhibit DNA topoisomerase II and the inhibitory effect on DNA topoisomerase II contributes to a high cytotoxicity. The introduction of an aminoalkoxy group at 1-position of DPT enhances the inhibitory activity against DNA topoisomerase II and cytotoxic effect, causing the inhibitory activity against tubulin polymerization to disappear. The results of antitumor test in mice bearing L 1210 on podophyllotoxin derivatives suggest the following: 1) the strong cytotoxic effect itself is not a good indication of antitumor activity in vivo as long as it is associated with inhibition of tubulin polymerization. DNA topoisomerase II inhibitory effect contributes to an antitumor activity in vivo; 2) detailed measurements of cytotoxicity and inhibition on DNA topoisomerase II and tubulin polymerization in vitro are necessary to evaluate podophyllotoxin derivatives.     

Use of immobilized triazine dyes in the purification of DNA topoisomerase I (Topo I) and terminal deoxynucleotidyl transferase (TdT) from calf thymus.

The interaction between TdT and Topo I, and twelve various triazine dyes immobilized on Sepharose CL-6B was studied. Yellow lightproof 2KT-Sepharose and Bordeaux 4ST-Sepharose were used to purify TdT and Topo I, respectively. The principal role of copper ions, complexed to the dye molecules, in the dye-protein interaction was evaluated.     

Multiple and irreversible binding of cis-diamminedichloroplatinum(II) to human serum albumin and its effect on warfarin binding.

Irreversible bindings of cis-diamminedichloroplatinum(II) (cis-DDP) to human serum albumin (HSA) were investigated in a pH 7.4 buffer containing 0.1 M NaCl at various molar ratios (cis-DDP/HSA) up to 60 over a 14 d period (37 degrees C). The metal binding seemed to reach a plateau when incubated at less than 10 times excess of cis-DDP. As the molar ratio increased, the reaction rate was relatively fast within the first day, followed by a moderate increase in the metal binding. When incubated at 60 times excess of cis-DDP, the metal bound as much as 20 mol per mol of HSA in 14 d. Fluorescence quenching of the metal-bound protein suggested that the tryptophan residue was gradually exposed to a hydrophilic environment as the metal binding increased. Furthermore, cis-DDP cleaved disulfide bonds at the ratio of 1 mol of disulfide bond per 5.3 mol of the metal binding. It was therefore suggested that the metal binding also occurred at several sites other than the disulfide bond. Warfarin binding to the metal-bound protein, examined by fluorescence changes, also decreased with increasing metal binding or cleavage of the disulfide bonds. Thus, cis-DDP bound to multiple sites in addition to the lone sulfhydryl group (Cys-34), suggesting that massive conformational changes of the protein took place.