Targeting a prokaryotic protein in a eukaryotic pathogen: identification of lead compounds against cryptosporidiosis

Cryptosporidium parvum is an important human pathogen and potential bioterrorism agent. No vaccines exist against C. parvum, the drugs currently approved to treat cryptosporidiosis are ineffective, and drug discovery is challenging because the parasite cannot be maintained continuously in cell culture. Mining the sequence of the C. parvum genome has revealed that the only route to guanine nucleotides is via inosine-5'-monophosphate dehydrogenase (IMPDH). Moreover, phylogenetic analysis suggests that the IMPDH gene was obtained from bacteria by lateral gene transfer. Here we exploit the unexpected evolutionary divergence of parasite and host enzymes by designing a high-throughput screen to target the most diverged portion of the IMPDH active site. We have identified four parasite-selective IMPDH inhibitors that display antiparasitic activity with greater potency than paromomycin, the current gold standard for anticryptosporidial activity.     

Chemiluminescence from eukaryotic and prokaryotic cells: reducing potential and oxygen requirements.

Abstract— The postphagocytic microbicidal activity of polymorphonuclear leukocytes (PMNL), the effector phagocytes of the acute inflammatory response, is metabolically characterized by increased glucose oxidation via the hexose monophosphate shunt and by increased non-mitochondrial oxygen consumption. These metabolic alterations result from the phagocytic activation of a membrane-associated NADPH:O, oxidoreductase. The products of univalent reduction of O₂ by this enzyme, O^-₂ and H ⁺, may further react to yield potential microbicidal oxidants such as H₂O₂, OC1^--, OH, and ¹A_gO₂. The microbicidal activity of PMNL is associated with the generation of luminescence. This chemiluminescence correlates with the metabolic generation of reducing potential and O₂ consumption, and is proposed to originate from the relaxation of the electronically excited products of microbicidal oxidation. The importance of O₂ in microbicidal metabolism will be considered, and data demonstrating the O₂-dependence of PMNL-chemiluminescence are presented. The phenomenon of chemiluminescence from non-bioluminescent bacteria is also described, and preliminary data from luminescence studies of Streptococcus faecalis are presented. The relationship of light emission to bacterial metabolism and O₂ toxicity is considered. Evidence for the bacterial generation of O^-₂ is presented, and the role of O^-2 and H₂O₂ in oxidative reactions productive of electronic excited molecular products is discussed.     

Lunasin: a novel cancer preventive seed peptide that modifies chromatin

Lunasin is a novel cancer preventive peptide whose efficacy against chemical carcinogens and oncogenes has been demonstrated in mammalian cells and a skin cancer mouse model. In contrast, constitutive expression of the lunasin gene in mammalian cells leads to arrest of cell division and cell death. Isolated and characterized in soy, lunasin peptide is also documented in barley and wheat and is predicted to be present in many more seeds because of its possible role in seed development. Initial studies show that lunasin is bioavailable in mice when orally ingested. Lunasin internalizes into mammalian cells within minutes of exogenous application, and localizes in the nucleus after 18 h. It inhibits acetylation of core histones in mammalian cells but does not affect the growth rate of normal and established cancer cell lines. An epigenetic mechanism of action is proposed whereby lunasin selectively kills cells being transformed or newly transformed cells by binding to deacetylated core histones exposed by the transformation event, disrupting the dynamics of histone acetylation-deacetylation.     

Novel electrochemical sensor system for monitoring metabolic activity during the growth and cultivation of prokaryotic and eukaryotic cells

A novel amperometric sensor system is presented which directly reflects the metabolic activity of prokaryotic and eukaryotic cells during cultivation. The principle of an externally mounted sensor is current measurement using a three-electrode system. Only living cells are detected since the current signal is based on a redox mediator. Added to a culture sample in its oxidized form, the mediator is reduced by cellular metabolism and subsequently re-oxidized at the anode. The spontaneous immobilisation of the cells in the reaction vessel of the sensor by swelling dextrane polymers (Sephadex) prior to measurement is the key to a fast, consistent signal. Even metabolically less active mammalian cells produce a reliable signal within a few minutes; this may open up future applications of the electrochemical sensor in closed loop process control not only for bacterial and fungal bioprocesses, but also in cell culture technology.     

A novel coenzyme NADH model 1-benzyl-1,4-dihydronicotinamide-mediated reaction: a single intermediate serves two mechanisms

Thermal reaction of ethyl (2Z)-4-bromo-2-cyano-3-(2-naphthyl)but-2-enoate (BCNB) with coenzyme NADH model 1-benzyl-1,4-dihydronicotinamide (BNAH) gives the debrominated cyclized product (E)-1-cyano-2-methyl-2-(2-naphthyl)cyclopropane-1-carboxylate (1), debrominated olefinic products ethyl (2E)-2-cyano-3-(2-naphthyl)but-2-enoate (2) and ethyl (2Z)-2-cyano-3-(2-naphthyl)but-2-enoate (3). The formation of 1 proceeds via partial concerted hydride transfer and debromocyclopropanation, whereas the formation of 2 or 3 proceeds via an electron transfer-debromination-hydrogen abstraction mechanism. Nonetheless, they all derived from the same electron-transfer intermediate complex.     

Relaxation mode analysis of a peptide system: comparison with principal component analysis

This article reports the first attempt to apply the relaxation mode analysis method to a simulation of a biomolecular system. In biomolecular systems, the principal component analysis is a well-known method for analyzing the static properties of fluctuations of structures obtained by a simulation and classifying the structures into some groups. On the other hand, the relaxation mode analysis has been used to analyze the dynamic properties of homopolymer systems. In this article, a long Monte Carlo simulation of Met-enkephalin in gas phase has been performed. The results are analyzed by the principal component analysis and relaxation mode analysis methods. We compare the results of both methods and show the effectiveness of the relaxation mode analysis.     

The thiosulfinyl group serves as a stereogenic center and shows diamagnetic anisotropy similar to that of the sulfinyl group

The pseudotetrahedral geometry of the thiosulfinyl group (>S=S) in the thionosulfite which was prepared by treatment of cis-3,4-di-tert-butylthiolane-3,4-diol with 1,1'-thiobisbenzimidazole is stable enough to allow the isolation of two diastereomers. X-ray crystallographic analysis revealed that the configuration of the >S=S group of the major diastereomer (45% isolated yield) is syn to the thiolane ring, while that of the minor diastereomer (10% isolated yield) is anti to the thiolane ring. 1H NMR spectrum analysis clarified that the shielding and deshielding zones of the >S=S group are similar to those of the >S=O group. Chemical properties of the >S=S group toward thermolysis, hydrolysis, and oxidation were clarified. The absorptions or bands in the UV/vis, IR, and Raman spectra, which originate from the >S=S group, were assigned on the basis of the B3LYP/6-31G* level calculations.     

Diastereoselective synthesis of a novel phosphinic peptide as ACE inhibitor: Fragment-based design approach

In medicinal chemistry for the purpose of lead optimization, hit selection of new isofunctional chemotypes are crucial for the success of identifying novel chemical entities of increased potency. Using fragment-based design approach with the N-selective inhibitor RXP407, a novel phosphinic peptide scaffold that consisted of modified RXP407 fragments was generated. The presented synthetic route is straightforward and produces the desired product Z-RXP407 in moderate yield. The (S,R,S,S)-Z-RXP407 analog has been evaluated for the C- and N-domain constructs of angiotensin-converting enzyme. The potency of this analog has been much lower compared to the parent compound RXP407, providing thus valuable insights regarding further design based on structure–activity relationships.     

Synthesis of mannose-containing neoglycolipids as a component of targeted delivery system for transfer of nucleic acids into antigen-presenting cells

Two approaches to the preparation of mannose-containing neoglycolipid, designed for development of nonviral targeted delivery system for transfer of nucleic acids into antigen-presenting cells, were described. They differed from each other in the binding of the targeting ligand and the lipid anchor, which was effected either through the formation of an amide bond or via the chemoselective binding agent 3,4-diethoxycyclobut-3-ene-1,2-dione.     

Structure and conformational features of tetrahydrothienothiepinoisoxazole as a novel heterocyclic system

The crystal and molecular structure of a novel heterocyclic system, 8-methyl-3,3a,4,5-tetrahydrothieno[3,2:6,7]thiepino[4,5-c]isoxazole, has been determined by X-ray analysis. The seven-membered ring has the boat conformation (B), while the isoxazoline cycle has the flat chair conformation (₃E). There are strong steric strains between the vicinal protons at the C(3a), C(3), and C(4) atoms.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 10, pp. 1795–1797, October, 1994.     

Manadomanzamines A and B: a novel alkaloid ring system with potent activity against mycobacteria and HIV-1

Two novel alkaloids, named manadomanzamines A (1) and B (2), were isolated from an Indonesian sponge Acanthostrongylophora sp. (Haplosclerida: Petrosiidae). Their structures were elucidated and shown to be a novel organic skeleton related to the manzamine type alkaloids. Their absolute configuration and conformation were determined by CD, NOESY, and molecular modeling analysis. The microbial community analysis for the sponge that produces these unprecedented alkaloids has also been completed. Manadomanzamines A (1) and B (2) exhibited strong activity against Mycobacterium tuberculosis (Mtb) with MIC values of 1.9 and 1.5 mug/mL, respectively. Manadomanzamines A and B also exhibit activities against human immunodeficiency virus (HIV-1) and AIDS opportunistic fungal infections.     

Development of a regenerable cell culture system that senses and releases dead cells

We developed a rapidly regenerable cell culture system in which the cell culture substrate detects cell death and selectively releases the dead cells. This culture material was achieved by combining a detector that responds to the signal from the dead cells and an actuator to release the dead cells. Benzo-18-crown-6-acrylamide (BCAm) with a pendant crown ether receptor was used as the sensor to recognize cellular signals and N-isopropylacrylamide (NIPAM) was used as the actuator. This copolymer of NIPAM and BCAm can respond to potassium ions and change its nature from hydrophobic to hydrophilic at the culture temperature of 37 degrees C. Living cells concentrate potassium ion internally; when cells die, potassium ions are released. The polymer surface recognizes the potassium ions released from the dead cells, the NIPAM hydrates, and the dead cells are selectively detached. This in vitro culture system is a novel one in which artificial culture materials work cooperatively with cellular metabolism by responding to this signal from the cells, thereby realizing in vitro tissue regeneration partly mimicking the mechanisms of in vivo homeostasis.     

TBD/Al2O3: a novel catalytic system for dynamic intermolecular aldol reactions that exhibit complex system behaviour

The heterogeneous system TBD/Al(2)O(3) is an efficient catalyst for the intermolecular aldol reaction between ketones and aromatic aldehydes. This system operates with low catalysts loading (10%), in water or organic solvents, and with short reaction times. The desired aldol products are rendered cleanly. Experiments confirmed that this aldol protocol is reversible, and allowed for the preparation of dynamic combinatorial libraries (DCLs) of interconverting aldols. Analysis of these DCLs showed up how properties such as diastereoselectivity can emerge unpredictably from the library when it is considered as a whole.     

Dihydrocercosporin singlet oxygen production and subcellular localization: a possible defense against cercosporin phototoxicity in Cercospora

Fungi in the genus Cercospora produce cercosporin, a potent singlet oxygen (1O2)-generating photosensitizer that plays a critical role in the ability of these fungi to parasitize plants. Although plants, mice, bacteria and many fungi are sensitive to cercosporin, Cercospora species are resistant to its toxicity. The cellular resistance of these fungi to cercosporin has been correlated with fungal cell surface reducing ability and the ability to maintain cercosporin in a chemically reduced state. As a model for reduced cercosporin we employed a reduced, acetylated derivative (hexaacetyl-dihydrocercosporin, HAC) that we tested for 1O2 production in a range of solvents. We found that as a 1O2 photosensitizer, HAC was only moderately effective in organic solvents (phi SO = 0.14-0.18) and very poor in water (phi SO = 0.02-0.04). By contrast, the 1O2 quantum yield of cercosporin itself was unaffected by solvent (phi SO = 0.84-0.97). To investigate the localization of reduced cercosporin in fungal cells, we developed a fluorescence assay using laser scanning confocal microscopy. This assay showed a uniform green fluorescence, indicative of reduced cercosporin, in the cytoplasm of hyphal cells treated with cercosporin. We hypothesize that the main protection mechanism against cercosporin phototoxicity in the fungus consists of transformation of cercosporin to a reduced state and localization of this reduced form in the aqueous compartment of the cell, thus decreasing intracellular 1O2 production to levels that can be tolerated by the fungus. In addition, we have, for the first time, directly detected 1O2 phosphorescence from fungal culture, either stained with the photosensitizer rose bengal or actively synthesizing cercosporin, demonstrating 1O2 production in vivo and from cercosporin in culture.     

Self-assembled nanospheres as a novel delivery system for taxol: a molecular hydrogel with nanosphere morphology

Here we reported on the first example of a Folic acid-based molecular hydrogel with nanosphere morphology as a delivery system for Taxol.     

N-methyl-phenacyloxycarbamidomethyl (Pocam) group: a novel thiol protecting group for solid-phase peptide synthesis and peptide condensation reactions

In the so-called thioester method for the condensation of peptide segments, protecting groups for amino and thiol groups are required for chemoselective ligation. In this study, we developed a novel thiol protecting group, N-methyl-phenacyloxycarbamidomethyl (Pocam). We used it for protection of cysteine side chains, and synthesized Pocam-containing peptides and peptide thioesters. These were condensed by the thioester method. After the condensation reaction, Pocam groups were cleaved by Zn/AcOH treatment. At the same time, the azido group, which was used for the protection of lysine side chains, was also converted to an amino group, demonstrating that this protecting group strategy simplified the deprotecting reaction after the peptide condensation reaction to only one step.     

Combinatorial library of peptide isosters based on Diels-Alder reactions: identification of novel inhibitors against a recombinant cysteine protease from Leishmania mexicana

A combinatorial split-and-mix library of peptide isosters based on a Diels-Alder reaction was synthesized as a "one-bead-two-compounds" library and encoded by ladder synthesis for facile analysis by matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry. In the "one-bead-two-compounds" library approach, each bead contains a library member as a putative protease inhibitor along with a fluorescence-quenched substrate for the protease. When the library was screened with CPB2.8 DeltaCTE, a recombinant cysteine protease from L. mexicana, several beads containing compounds with inhibitory activity could be selected from the library and analyzed by MALDI-TOF MS for structure elucidation. Two types of inhibitors were revealed. One novel class of inhibitors had the bicyclic Diels-Alder product isosteric element incorporated internally in a peptide, while the other type was an N-terminal alpha,beta-unsaturated ketone Michael acceptor used as starting material for the Diels-Alder reaction. Selected hit sequences and constructed consensus sequences based on the observed frequencies of amino acids in different subsites were resynthesized and assayed in solution for inhibitor activity and were shown to have IC(50) values in the high nanomolar to low micromolar range.     

N-methylformamide-benzene complex as a prototypical peptide N-H...pi hydrogen-bonded system: density functional theory and MP2 studies

Although the existence of peptide N-H...pi hydrogen bonds recently has been reported in protein structures, little is known about their strength and binding nature and, therefore, the relative importance of the interaction. To shed light on this binding, the N-methylformamide-benzene complex, as a model of the peptide N-H...pi hydrogen bonding, was studied by using density functional theory and M?ller-Plesset second-order perturbation (MP2) methods. The geometry of the complex was fully optimized at the B3LYP/6-31G(d,p) and MP2/6-31G(d,p) levels. The optimized interaction distances are about 3.6 and 3.2 A, respectively, at the two levels. The binding energy corrected by basis set superposition error with the MP2/cc-pVTZ method based on the MP2/6-31G geometry is -4.37 kcal/mol, which is as strong as the conventional hydrogen bonding. The calculated results suggest that the peptide N-H...pi hydrogen bonding is of sufficient strength to play an important role in the stabilization of protein structures. These results are helpful to better understand the characteristics and nature of the peptide N-H...pi interaction as well as to modify current force fields to better represent this special interaction.     

Evaluation of the binding ability of a novel dioxatetraazamacrocyclic receptor that contains two phenanthroline units: selective uptake of carboxylate anions

The novel dioxatetraaza macrocycle [26]phen2N4O2, which incorporates two phenanthroline units, has been synthesized, and its acid-base behavior has been evaluated by potentiometric and 1H NMR methods. Six protonation constants were determined, and the protonation sequence was established by NMR. The location of the fifth proton on the phen nitrogen was confirmed by X-ray determinations of the crystal structures of the receptor as bromide and chloride salts. The two compounds have the general molecular formula {(H5[26]phen2N4O2)Xn(H2O)(5-n)}X(n-1) x mH2O, where X = Cl, n = 3, and m = 6 or X = Br, n = 4, and m = 5.5. In the solid state, the (H5[26]phen2N4O2)(5+) cation adopts a "horseshoe" topology with sufficient room to encapsulate three or four halogen anions through the several N-H...X hydrogen-bonding interactions. Two supermolecules {(H5[26]phen2N4O2)Xn(H2O)5-n}(5-n)(+) form an interpenetrating dimeric species, which was also found by ESI mass spectrum. Binding studies of the protonated macrocycle with aliphatic (ox(2-), mal(2-), suc(2-), cit(3-), cta(3-)) and aromatic (bzc(-), naphc(-), anthc(-), pyrc(-), ph(2-), iph(2-), tph(2-), btc(3-)) anions were determined in water by potentiometric methods. These studies were complemented by 1H NMR titrations in D2O of the receptor with selected anions. The Hi[26]phen2N4O2(i+) receptor can selectively uptake highly charged or extended aromatic carboxylate anions, such as btc(3-) and pyrc(-), in the pH ranges of 4.0-8.5 and <4.0, respectively, from aqueous solution that contain the remaining anions as pollutants or contaminants. To obtain further insight into these structural and experimental findings, molecular dynamics (MD) simulations were carried out in water solution.     

A novel di-triazole based peptide as a highly sensitive and selective fluorescent chemosensor for Zn2+ ions

A di-triazole based peptide has been synthesised by copper catalyzed Huisgen cycloaddition. Fluorescence intensity is enhanced selectively in the presence of Zn(2+), which is ascribed to reversal of photoelectron transfer. Compound 7 was found to self-assemble in the presence of Zn(ClO(4))(2) in an exclusive 2:1 ratio, which is supported by (1)H NMR titration and mass spectral data. The fluorescence intensity of 7 shows a subsequent ON-OFF phenomenon upon repetitive and alternate addition of Zn(ClO(4))(2) and HClO(4).