Structure-Activity Relationships and Antiplasmodial Potencies of Novel 3,4-Disubstituted 1,2,5-Oxadiazoles

The 4-substituted 3-amino-1,2,5-oxadiazole 1 from the Malaria Box Project of the Medicines for Malaria Venture foundation shows very promising selectivity and in vitro activity against Plasmodium falciparum. Within the first series of new compounds, various 3-acylamino analogs were prepared. This paper now focuses on the investigation of the importance of the aromatic substituent in ring position 4. A number of new structure-activity relationships were elaborated, showing that antiplasmodial activity and selectivity strongly depend on the substitution pattern of the 4-phenyl moiety. In addition, physicochemical parameters relevant for drug development were calculated (logP and ligand efficiency) or determined experimentally (CYP3A4-inhibition and aqueous solubility). N-[4-(3-ethoxy-4-methoxyphenyl)-1,2,5-oxadiazol-3-yl]-3-methylbenzamide 51 showed high in vitro activity against the chloroquine-sensitive strain NF54 of P. falciparum (PfNF54 IC50 = 0.034 µM), resulting in a very promising selectivity index of 1526.

New Acyl Derivatives of 3-Aminofurazanes and Their Antiplasmodial Activities

An N-acylated furazan-3-amine of a Medicines for Malaria Venture (MMV) project has shown activity against different strains of Plasmodium falciparum. Seventeen new derivatives were prepared and tested in vitro for their activities against blood stages of two strains of Plasmodium falciparum. Several structure-activity relationships were revealed. The activity strongly depended on the nature of the acyl moiety. Only benzamides showed promising activity. The substitution pattern of their phenyl ring affected the activity and the cytotoxicity of compounds. In addition, physicochemical parameters were calculated (log P, log D, ligand efficiency) or determined experimentally (permeability) via a PAMPA. The N-(4-(3,4-diethoxyphenyl)-1,2,5-oxadiazol-3-yl)-3-(trifluoromethyl)benzamide possessed good physicochemical properties and showed high antiplasmodial activity against a chloroquine-sensitive strain (IC₅₀(NF54) = 0.019 µM) and even higher antiplasmodial activity against a multiresistant strain (IC₅₀(K₁) = 0.007 µM). Compared to the MMV compound, the permeability and the activity against the multiresistant strain were improved.

Heavy metals in agricultural soils of the European Union with implications for food safety

Soil plays a central role in food safety as it determines the possible composition of food and feed at the root of the food chain. However, the quality of soil resources as defined by their potential impact on human health by propagation of harmful elements through the food chain has been poorly studied in Europe due to the lack of data of adequate detail and reliability. The European Union's first harmonized topsoil sampling and coherent analytical procedure produced trace element measurements from approximately 22,000 locations. This unique collection of information enables a reliable overview of the concentration of heavy metals, also referred to as metal(loid)s including As, Cd, Cr, Cu, Hg, Pb, Zn, Sb. Co, and Ni. In this article we propose that in some cases (e.g. Hg and Cd) the high concentrations of soil heavy metal attributed to human activity can be detected at a regional level. While the immense majority of European agricultural land can be considered adequately safe for food production, an estimated 6.24% or 137,000km(2) needs local assessment and eventual remediation action.

Enhanced mobilization of the bone marrow-derived circulating progenitor cells by intracoronary freshly isolated bone marrow cells transplantation in patients with acute myocardial infarction

Autologous bone marrow cell transplantation (BMCs-Tx) is a promising novel option for treatment of cardiovascular disease. We analysed in a randomized controlled study the influence of the intracoronary autologous freshly isolated BMCs-Tx on the mobilization of bone marrow–derived circulating progenitor cells (BM-CPCs) in patients with acute myocardial infarction (AMI). Sixty-two patients with AMI were randomized to either freshly isolated BMCs-Tx or to a control group without cell therapy. Peripheral blood (PB) concentrations of CD34/45⁺- and CD133/45⁺-circulating progenitor cells were measured by flow cytometry in 42 AMI patients with cell therapy as well as in 20 AMI patients without cell therapy as a control group on days 1, 3, 5, 7, 8 and 3, 6 as well as 12 months after AMI. Global ejection fraction (EF) and the size of infarct area were determined by left ventriculography. We observed in patients with freshly isolated BMCs-Tx at 3 and 12 months follow up a significant reduction of infarct size and increase of global EF as well as infarct wall movement velocity. The mobilization of CD34/45⁺ and CD133/45⁺ BM-CPCs significantly increased with a peak on day 7 as compared to baseline after AMI in both groups (CD34/45⁺: P < 0.001, CD133/45⁺: P < 0.001). Moreover, this significant mobilization of BM-CPCs existed 3, 6 and 12 months after cell therapy compared to day 1 after AMI. In control group, there were no significant differences of CD34/45⁺ and CD133/45⁺ BM-CPCs mobilization between day 1 and 3, 6 and 12 months after AMI. Intracoronary transplantation of autologous freshly isolated BMCs by use of point of care system in patients with AMI may enhance and prolong the mobilization of CD34/45⁺ and CD133/45⁺ BM-CPCs in PB and this might increase the regenerative potency after AMI.

Biopharmaceutical characterization of some new papaverine decomposition products

2,3,9,10-Tetramethoxy-12-oxo-12-H-indolo[2,1-a]isoquinolinium chloride 1 (compound X) and 13-(3,4-dimethoxyphenyl)-2,3,8,9-tetramethoxy-6a, 12a-diazadibenzo[a,g] fluorenylium chloride 2 (compound NF) are new papaverine oxidation products. A solution of compound 1 bleaches on addition of sodium hydroxide solution. A new entity, 2-(2-carboxy-4,5-dimethoxyphenyl)-6,7-dimethoxyisoquinolinium inner salt 3 (compound WP), is formed. The physico-chemical properties of compounds 1-3, such as solubility in water and lipophilicity, have been measured. The IC50 for compounds 1 and 3 was also assessed.

Mechanism and Regulation of Isoleucine Excretion in Corynebacterium glutamicum

Whole cells of Corynebacterium glutamicum were loaded with high cytoplasmic l-isoleucine concentrations, and isoleucine excretion from these cells was studied in terms of mechanism and regulation. The transmembrane isoleucine flux could be differentiated into carrier-mediated uptake, carrier-mediated excretion, and diffusion. After discrimination from the other transmembrane solute movements, the outward-directed flux, which was due to the activity of the isoleucine excretion carrier, was characterized with respect to its energy dependence and its regulation at the level of expression. Isoleucine excretion was shown to function as a secondary transport process, driven by the membrane potential and coupled to the movement of protons, presumably with a stoichiometry of 2:1 (H(sup+)/isoleucine). Of a variety of putative transport substrates, only leucine was able to compete for isoleucine at the cis (cytosolic) side of the export carrier. Cytoplasmic isoleucine concentrations higher than 20 mM induce the activity of the isoleucine excretion system. This effect is specific for isoleucine and is inhibited by the presence of chloramphenicol. Apart from leucine, other amino acids and related amino acid analogs are not able to induce isoleucine excretion. The complex pattern of regulation of the isoleucine excretion system at the level of activity and expression is shown to be related to the pattern of regulation of the isoleucine uptake system in C. glutamicum in terms of physiological significance.

Partition coefficients of some purine derivatives and its application to pharmacokinetics

Metazathioprine (MAZA), a methylated derivative of azathioprine (AZA), demonstrated the greatest values of apparent and specific partition coefficients in n-octanol/phosphate buffer at pH 5.7 and pH 7.4 among purine derivatives such as 6-mercaptopurine (6-MP), 6-thioguanine (6-TG) and AZA. Introduction of a methyl group into the imidazole ring of AZA increases lipophilic properties of MAZA compared to AZA. Mass balance of purine derivatives in n-octanol and in phosphate buffer indicated their chemical stability in those media.

Electron ionisation mass spectral study of 2-(2-carboxy-4, 5-dimethoxyphenyl)-6,7-dimethoxyisoquinolinium inner salt

The electron ionization mass spectrum of 2-(2-carboxy-4,5-dimethoxyphenyl)-6,7-dimethoxyisoquinolinium inner salt 1 is discussed and general fragmentation routes of its molecular ion are proposed. Comparison of the data obtained for 1 with the EI-MS data of metameric protopine alkaloids (allocryptopine, argemexicaine A, argemexicaine B) and the pseudobenzyloisoquinoline alkaloid taxilamine allows a differentiation between these metamers. The data will be useful for the identification of metabolites of alkaloids of these types in biological matrices.

Aminoglycoside antibiotics: old drugs and new therapeutic approaches

Aminoglycoside antibiotics kill bacteria by binding to the ribosomal decoding site and reducing fidelity of protein synthesis. Since the discovery of these natural products over 50 years ago, aminoglycosides have provided a mainstay of antibacterial therapy of serious Gram-negative infections. In recent years, aminoglycosides have become important tools to study molecular recognition of ribonucleic acid (RNA). In an ingenious exploitation of the aminoglycosides' mechanism of action, it has been speculated that drug-induced readthrough of premature stop codons in mutated messenger RNAs might be used to treat patients suffering from certain heritable genetic disorders.

A-site model RNAs

Oligonucleotide model systems have played a key role for the exploration of structure, dynamics and ligand binding of the ribosomal decoding-site (A site). An overview is given on the merits and limitations of various A-site models that were used for solution and crystallographic work.

Biomarker correlates of survival in NSCLC: Role of RXRβ and PPARγ in mediating bexarotene impact on patient survival

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Background: Bexarotene is a selective modulator of retinoid X nuclear receptors (RXRs), which form heterodimers with many other nuclear receptors playing a critical role in cell growth, differentiation, and apoptosis. Loss of RXRs is seen in many advanced tumors, including NSCLC and higher RXR levels in NSCLC lung biopsies (stages I-III) have been correlated with longer overall survival. Two large first line NSCLC Phase III trials reported at ASCO 2005 (SPIRIT I and II) showed that while no benefit in overall survival was seen adding bexarotene to two chemo regimens, a large (36%) subpopulation of patients in both trials that had high grade hypertriglyceridemia in response to bexarotene had significantly longer survival. A retrospective analysis was conducted to evaluate the baseline characteristics of these patients and to examine the level of expression of RXR and one of its partners (PPARγ) in lung tumor tissue biopsies obtained from a subgroup of patients in both studies. Methods: RXRs (α,β,γ) and PPARγ expression levels in lung tumor tissue from patients in SPIRIT I and II trials (stage IIIB/IV) taken prior to study entry were assessed by Q-PCR analysis of RNA isolated from microdissected lung tumor tissue biopsies. Cox regression and Kaplan-Meier survival estimation were used for statistical evaluations. Results: In an initial subset of 41 patients, RXRβ expression in lung tumor showed positive correlation with survival. High RXRβ = longer survival (median survival 438 days), low RXR shorter (MS = 317). Treatment with bexarotene increased the differences (RXRβ Hi, MS = 627 days; RXRβ low = 211 days). PPARγ showed a negative correlation with survival and those patients with RXRβ Hi/PPARγ low ratios had the longest MS (627 days vs. 226 days for the RXRβ low/PPARγ high group), a difference that was magnified by bexarotene treatment. Conclusions: RXRβ expression level correlates with a positive survival in late stage NSCLC while PPARγ shows negative correlation. Bexarotene treatment enhances the survival differences, supporting an involvement of triglyceride and lipid metabolism as regulated by these two key nuclear receptors in the longer survival seen in the 215 patients in the high triglyceride subgroup.

[Table: see text]

[Biological availability of ibuprofen in Imbun 500 suppositories]

Concentration of ibuprofen in rabbit blood was found to be considerably higher after application of Imbun-500 suppositories, containing 500 mg of ibuprofen lysine salt equivalent to 292.6 mg of free ibuprofen, than after application of ibuprofen dragees containing 400 mg of the free drug. Parameters characterizing biological availability of ibuprofen in Imbun-500 suppositories (AUC, Cmax, tmax) were determined. Ibuprofen lysine salt proved to be considerably more easily absorbed from suppositories than ibuprofen from dragees of either home or foreign production.

Biopharmaceutical characterization of some synthetic purine drugs

Hydrophilic-lipophilic properties (water solubility, n-octanol/water partition coefficient, transport across membranes) of some mercaptopurines (6-MP, 6-TG, AZA and a new AZA derivative--metazathioprine (MAZA) were determined. MAZA is the most lipophilic compound due to low aqueous solubility and high n-octanol/water partition coefficient. The fluxes from the donor medium into the membrane and from the membrane into the acceptor medium are highest for MAZA as well. The partition coefficients of the other purines decrease in the order: AZA > 6-TG > 6-MP.

Recommendations for the treatment of localized prostate cancer by permanent interstitial brachytherapy

The increasing use of interstitial brachytherapy for the treatment of prostate cancer has made it necessary to discuss and establish guidelines for the application of this treatment modality. A group of experts representing the four professional and scientific societies of urologic surgeons and radiation oncologists in Germany was formed by the German Society of Urology (Deutsche Gesellschaft für Urologie, DGU), the Association of German Urologists (Berufsverband der Deutschen Urologen e.V., BDU), the German Society for Radiation Oncology (Deutsche Gesellschaft für Radioonkologie, DEGRO) and the Association of German Radiotherapists (Berufsverband der Deutschen Strahlentherapeuten, BVDSt). This group has formulated a consensus statement consisting of recommendations and guidelines for the indications, planning, implementation and follow-up of permanent interstitial brachytherapy by seed implantation for the treatment of localized prostate cancer. These recommendations also define the responsibilities of the two medical disciplines involved in the use of this interdisciplinary treatment.

Carnitine palmitoyltransferase II deficiency: molecular and biochemical analysis of 32 patients

The authors investigated 32 patients with the muscle form of CPT II deficiency. Total carnitine palmitoyltransferase enzyme system (CPT) activity was normal but abnormally inhibited by malonyl-CoA, palmitoyl-CoA, and the detergents Triton X and Tween 20. Mutation analysis identified three described mutations (S113L, P50H, and F448L) and two novel mutations (M214T and Y479F). Using modeling techniques, a structure could be identified anchoring the protein in the membrane. Only one of the five mutations (Y479F) is located within this region.

Molecular characterization of Pax6(2Neu) through Pax6(10Neu): an extension of the Pax6 allelic series and the identification of two possible hypomorph alleles in the mouse Mus musculus

Phenotype-based mutagenesis experiments will increase the mouse mutant resource, generating mutations at previously unmarked loci as well as extending the allelic series at known loci. Mapping, molecular characterization, and phenotypic analysis of nine independent Pax6 mutations of the mouse recovered in mutagenesis experiments is presented. Seven mutations result in premature termination of translation and all express phenotypes characteristic of null alleles, suggesting that Pax6 function requires all domains to be intact. Of major interest is the identification of two possible hypomorph mutations: Heterozygotes express less severe phenotypes and homozygotes develop rudimentary eyes and nasal processes and survive up to 36 hr after birth. Pax6(4Neu) results in an amino acid substitution within the third helix of the homeodomain. Three-dimensional modeling indicates that the amino acid substitution interrupts the homeodomain recognition alpha-helix, which is critical for DNA binding. Whereas cooperative dimer binding of the mutant homeodomain to a paired-class DNA target sequence was eliminated, weak monomer binding was observed. Thus, a residual function of the mutated homeodomain may explain the hypomorphic nature of the Pax6(4Neu) allele. Pax6(7Neu) is a base pair substitution in the Kozak sequence and results in a reduced level of Pax6 translation product. The Pax6(4Neu) and Pax6(7Neu) alleles may be very useful for gene-dosage studies.

A high-resolution reference map for cytoplasmic and membrane-associated proteins of Corynebacterium glutamicum

We present a high-resolution reference map for soluble proteins obtained from Corynebacterium glutamicum cells grown in glucose minimal medium. The analysis window covers the pl range from 4-6 and the molecular mass range from 5-100 kDa. Using overlapping narrow immobilized pH gradients for isoelectric focusing, 970 protein spots were detected after second-dimensional separation on SDS-polyacrylamide gels and colloidal Coomassie-staining. By tryptic peptide mass fingerprinting 169 protein spots were identified, representing 152 different proteins including many enzymes involved in central metabolism (18), amino acid biosynthesis (24) and nucleotide biosynthesis (11). Thirty-five of the identified proteins have no known function. A comparison of the observed and the expected physicochemical properties of the identified proteins indicated that nine proteins were covalently modified, since variants with apparently identical molecular mass, but differing pl were detected. The N-termini of eight proteins were determined by post-source decay (PSD) analysis of selected peptides. In addition to the soluble proteins, a map of the membrane-bound proteins within the pl range 4-7 is presented, which contains 660 protein spots, 22 of which were identified, representing 13 different proteins.

Mechanism of activation of an immunosuppressive drug: azathioprine. Quantum chemical study on the reaction of azathioprine with cysteine

Azathioprine is an important drug used in the therapy of autoimmune disorders and in preventing graft rejection. Its molecule is composed of two main moieties: mercaptopurine and imidazole derivative. It is an immunosuppressive agent whose biological activity results from its in vivo mercaptolysis mediated by a nucleophilic attack on the C(5i) atom of imidazole ring of the azathioprine molecule. Solvation model SM5.4 with the PM3 Hamiltonian have been applied to model the reaction of azathioprine with cysteine. The employed quantum mechanical method shed new light on the mechanism of the reaction of azathioprine with cysteine in aqueous solution. The obtained results indicated that the first step in the reaction most likely involves the nucleophilic attack of the COO(-) of cysteine on the C(5i) atom of the imidazole ring of azathioprine, followed by a subsequent intramolecular attack of the SH group of the cysteine residue. It was shown that biogenic thiols such as glutathione or cysteine facilitate the first and crucial step of azathioprine metabolism, due to the presence of COO(-), SH, and NH(3)(+) groups in their molecules.

Proteome analysis of Corynebacterium glutamicum

By the use of different Corynebacterium glutamicum strains more than 1.4 million tons of amino acids, mainly L-glutamate and L-lysine, are produced per year. A project was started recently to elucidate the complete DNA sequence of this bacterium. In this communication we describe an approach to analyze the C. glutamicum proteome, based on this genetic information, by a combination of two-dimensional (2-D) gel electrophoresis and protein identification via microsequencing or mass spectrometry. We used these techniques to resolve proteins of C. glutamicum with the aim to establish 2-D protein maps as a tool for basic microbiology and for strain improvement. In order to analyze the C. glutamicum proteome, methods were established to fractionate the C. glutamicum proteins according to functional entities, i.e., cytoplasm, membranes, and cell wall. Protein spots of the cytoplasmic and membrane fraction were identified by N-terminal sequencing, immunodetection, matrix assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF-MS) and electrospray ionization-mass spectrometry (ESI-MS). Additionally, a protocol to analyze proteins secreted by C. glutamicum was established. Approximately 40 protein spots were observed on silver-stained 2-D gels, 12 of which were identified.

Peptide-triggered conformational switch in HIV-1 RRE RNA complexes

We have used NMR spectroscopy to determine the solution structure of a complex between an oligonucleotide derived from stem IIB of the Rev responsive element (RRE-IIB) of HIV-1 mRNA and an in vivo selected, high affinity binding Arg-rich peptide. The peptide binds in a partially alpha-helical conformation into a pocket within the RNA deep groove. Comparison with the structure of a complex between an alpha-helical Rev peptide and RRE-IIB reveals that the sequence of the bound peptide determines the local conformation of the RRE peptide binding site. A conformational switch of an unpaired uridine base was revealed; this points out into the solvent in the Rev peptide complex, but it is stabilized inside the RNA deep groove by stacking with an Arg side chain in the selected peptide complex. The conformational switch has been visualized by NMR chemical shift mapping of the uridine H5/H6 atoms during a competition experiment in which Rev peptide was displaced from RRE-IIB by the higher affinity binding selected peptide.

Induction of adipocyte-specific gene expression is correlated with mammary tumor regression by the retinoid X receptor-ligand LGD1069 (targretin)

Targretin (LGD1069; a high-affinity ligand for the retinoid X receptors) is an efficacious chemotherapeutic and chemopreventive agent in the N-nitroso-N-methylurea-induced rat mammary carcinoma model. To evaluate the molecular action of LGD1069 in mammary carcinoma we have examined gene expression patterns in controls and nonresponding tumors compared with tumors undergoing regression (responding) by LGD1069. When compared with controls or nonresponding tumors, the expression of adipocyte-related genes such as adipocyte P2 (aP2), adipsin, peroxisome proliferator-activated receptor gamma (PPARgamma), and lipoprotein lipase was elevated in LGD1069-responding tumors. Further analysis showed that gene expression changes occurred rapidly, in as little as 6 h, after the first dose of LGD1069. Immunohistochemical analysis showed that aP2 protein was also highly expressed in responding tumors when compared with control or nonresponding tumors. More importantly, aP2 protein was localized in the tumor cells in addition to the adipocytes present in the tumors. Similar changes in gene expression and inhibition in growth were seen in tumor cells (cloned from N-nitroso-N-methylurea-induced carcinoma) exposed to LGD1069 in vitro. These data suggest that tumor regression by LGD1069 involves differentiation induction along the adipocyte lineage.

Exposure of human endometrium to environmental estrogens, antiandrogens, and organochlorine compounds

OBJECTIVE

To determine concentrations of environmental estrogens, antiandrogens, and organochlorine compounds in human endometrium and body fat.

DESIGN

Cross-sectional, population-based study.

SETTING

Patient recruitment was done at a university hospital; chemical analysis was performed in a specialized private laboratory.

PATIENT(S)

Premenopausal, unexposed women undergoing hysterectomy for uterine myoma.

INTERVENTION(S)

None.

MAIN OUTCOME MEASURE(S)

Concentrations of environmental modulators in human endometrium and body fat were quantified by high-resolution gas chromatography/high-resolution mass spectrometry.

RESULT(S)

Among known endocrine modulators, the antiandrogenic p, p'-dichlorodiphenyl-dichloroethylene was found in the highest concentrations in endometrium (median 4.7 microg/kg wet weight) and body fat (median 446 microg/kg wet weight). Only trace amounts of the identified environmental estrogens beta-hexachlorocyclohexane, o, p'-dichlorodiphenyl-trichloroethane, bisphenol A, hydroxylated polychlorinated biphenyls, and genistein were found in the endometrium (median <1 microg/kg wet weight). As major organochlorine contaminants without endocrine activities, polychlorinated biphenyls and hexachlorobenzene were found.

CONCLUSION(S)

Our data demonstrate that nonchlorinated environmental estrogens do not build up cumulative tissue concentrations in the endometrium. The risk of reduced fertility because of ambient levels of environmental estrogens in the endometrium is negligible.

Molecular dynamics investigations of hammerhead ribozyme RNA

The hammerhead ribozyme, a small catalytic RNA molecule, cleaves, in the presence of magnesium ions, a specific phosphodiester bond within its own backbone, leading to 23-cyclic phosphate and 5-OH extremities. In order to study the dynamical flexibility of the hammerhead RNA, we performed molecular dynamics simulations of the solvated crystal structure of an active hammerhead ribozyme, obtained after flash-freezing crystals soaked with magnesium. Because of a careful equilibration protocol and the use of the Ewald summation in calculating the electrostatic interactions, the RNA structure remained close to the crystal structure, as attested by a root-mean-square deviation below 2.5 A after 750 ps of simulation. All Watson-Crick base pairs were intact at the end of the simulations. The tertiary interactions, such as the sheared G.A pairs and the U-turn, important for the stabilisation of the three-dimensional RNA fold, were also retained. The results demonstrate that molecular dynamics simulations can be successfully used to investigate the dynamical behaviour of a ribozyme, thus, opening a road to study the role of transient structural changes involved in ribozyme catalysis.

Saccharide-RNA recognition

Among saccharides, the antibiotics of the aminoglycoside family are the best-studied class of molecules interacting with RNA. By binding to RNA targets, aminoglycosides act as inhibitors of protein biosynthesis, they interfere with protein-RNA interaction of retroviral regulatory elements, and they inhibit the catalytic action of ribozymes. Here, we survey the available data on molecular structural details of aminoglycoside-RNA interaction.

Strategies for the Design of Drugs Targeting RNA and RNA-Protein Complexes

In many steps of gene replication and expression, RNA molecules participate as key players, which renders them attractive targets for therapeutic intervention. While the function of nucleic acids as carriers of genetic material is based on their sequence, a number of important RNAs are involved in processes that depend on the defined three-dimensional structures of these molecules. As for proteins, numerous complex folds of RNA exist. The development of drugs that bind specifically to RNA folds opens exciting new ways to expand greatly the existing repertoire of protein-targeted therapeutics. Most functions of RNAs involve interactions with proteins that contain RNA-binding domains. Effector molecules targeted at RNA may either alter the functional three-dimensional structure of the nucleic acid, so the interaction with proteins is thereby inhibited or enhanced, or, as interface inhibitors, they may directly prevent the formation of competent RNA-protein complexes. While the same tools used for the design of protein-targeted drugs may be considered for studying effectors binding to nucleic acids, the differences between proteins and RNAs in the forces which dominate their three-dimensional folding call for novel drug design strategies. In the present review, I will outline how our rapidly expanding knowledge of RNA three-dimensional structure and function facilitates rational approaches to develop RNA-binding compounds. Putative RNA targets for therapeutic intervention will be discussed along with recent advances in understanding RNA-small molecule and RNA-protein interactions.

Response to nitrogen starvation in Corynebacterium glutamicum

Proteins strongly synthesized in Corynebacterium glutamicum during nitrogen restriction were examined by two-dimensional gel electrophoresis and microsequencing. Two main groups of enzymes were identified beside miscellaneous proteins, enzymes involved (i) in protein synthesis, and (ii) in carbon metabolism. Biochemical measurements revealed an increase of oxygen consumption during nitrogen starvation, indicating an enhanced energy demand of the cells. By Northern hybridizations, an increased transcription for the gap and fda genes upon nitrogen deprivation was shown.

Rational drug design and high-throughput techniques for RNA targets

RNA molecules are the only known molecules which possess the double property of being depository of genetic information, like DNA, and of displaying catalytic activities, like protein enzymes. RNA molecules intervene in all steps of gene expression and in many other biological activities. Like proteins, RNAs achieve those biological functions by adopting intricate three-dimensional folds and architectures. Further, as in protein sequences, RNA sequences contain signatures specific for three-dimensional motifs which participate in recognition and binding. In regulatory pathways, RNA molecules exist in equilibria between transient structures differentially stabilized by effectors such as proteins or cofactors. Therefore, RNA molecules display their potential as drug targets on different levels, namely in three-dimensional folds, in structural equilibria and in RNA-protein interfaces. Several examples will be described together with the already available techniques for combinatorial synthesis and high-throughput screening of potential drug and target RNA molecules.

Doppler examinations in the prognosis of birth status of the newborn

AIM OF THE STUDY

Determination of correlation between Doppler parameters in the evaluation of fetal state and biochemical and clinical determinants of birth status of the newborn.

MATERIAL

30 full-term pregnancies.

METHODS

Doppler parameters were determined in maternal vessels (uterine and arcuate arteries), fetal vessels (middle cerebral arteries, renal artery and descending aorta) and in umbilical arteries and veins. Levels of uric acid, xanthine and hypoxanthine, which reflect oxygen deficiency, were assessed in amniotic fluid by means of HPLC method. Furthermore, clinical condition of a newborn (rating according to the Apgar scoring system), pH-metry and gasometry in umbilical blood were assessed.

RESULTS

Significant correlation between determinants of fetal and neonatal condition and Doppler parameters were determined, that is: between uric acid concentration and blood flow in fetal cerebral arteries, between base excess, pH and blood flow in umbilical vessels, between clinical examination of birth status of the newborn and renal and arcuate arterial flow and between pO2 and S/D ratio in renal artery.

CONCLUSIONS

On the basis of this correlation, the following conclusions were drawn: Doppler examinations are highly useful in the prediction of birth status of the newborn if the specific conditions and appropriate range of the examination are maintained, i.e.: 1) examination must be multivascular, 2) it should involve cerebral artery, parenchymal resistance vessels (for example renal artery), umbilical artery and vein, intramural uterine vessels (for example arcuate or spiral artery), 3) among blood flow parameters not only standard indices (S/D, RI, PI), but also arterial blood flow waves velocity, specific flow and transverse section field should be considered.

A dimeric DNA interface stabilized by stacked A.(G.G.G.G).A hexads and coordinated monovalent cations

We report on the identification of an A.(G.G.G.G).A hexad pairing alignment which involves recognition of the exposed minor groove of opposing guanines within a G.G.G.G tetrad through sheared G.A mismatch formation. This unexpected hexad pairing alignment was identified for the d(G-G-A-G-G-A-G) sequence in 150 mM Na(+) (or K(+)) cation solution where four symmetry-related strands align into a novel dimeric motif. Each symmetric half of the dimeric "hexad" motif is composed of two strands and contains a stacked array of an A.(G.G.G.G).A hexad, a G.G.G.G tetrad, and an A.A mismatch. Each strand in the hexad motif contains two successive turns, that together define an S-shaped double chain reversal fold, which connects the two G-G steps aligned parallel to each other along adjacent edges of the quadruplex. Our studies also establish a novel structural transition for the d(G-G-A-G-G-A-N) sequence, N=T and G, from an "arrowhead" motif stabilized through cross-strand stacking and mismatch formation in 10 mM Na(+) solution (reported previously), to a dimeric hexad motif stabilized by extensive inter-subunit stacking of symmetry-related A.(G.G.G.G).A hexads in 150 mM Na(+) solution. Potential monovalent cation binding sites within the arrowhead and hexad motifs have been probed by a combination of Brownian dynamics and unconstrained molecular dynamics calculations. We could not identify stable monovalent cation-binding sites in the low salt arrowhead motif. By contrast, five electronegative pockets were identified in the moderate salt dimeric hexad motif. Three of these are involved in cation binding sites sandwiched between G.G.G. G tetrad planes and two others, are involved in water-mediated cation binding sites spanning the unoccupied grooves associated with the adjacent stacked A.(G.G.G.G).A hexads. Our demonstration of A.(G. G.G.G).A hexad formation opens opportunities for the design of adenine-rich G-quadruplex-interacting oligomers that could potentially target base edges of stacked G.G.G.G tetrads. Such an approach could complement current efforts to design groove-binding and intercalating ligands that target G-quadruplexes in attempts designed to block the activity of the enzyme telomerase.

RNA bulges as architectural and recognition motifs

RNA bulges constitute versatile structural motifs in the assembly of RNA architectures. Three-dimensional structures of RNA molecules and their complexes reveal the role of bulges in RNA architectures and illustrate the molecular mechanisms by which they confer intramolecular interactions and intermolecular recognition.

Adaptive recognition by nucleic acid aptamers

Nucleic acid molecules play crucial roles in diverse biological processes including the storage, transport, processing, and expression of the genetic information. Nucleic acid aptamers are selected in vitro from libraries containing random sequences of up to a few hundred nucleotides. Selection is based on the ability to bind ligand molecules with high affinity and specificity. Three-dimensional structures have been determined at high resolution for a number of aptamers in complex with their cognate ligands. Structures of aptamer complexes reveal the key molecular interactions conferring specificity to the aptamer-ligand association, including the precise stacking of flat moieties, specific hydrogen bonding, and molecular shape complementarity. These basic principles of discriminatory molecular interactions in aptamer complexes parallel recognition events central to many cellular processes involving nucleic acids.

Two-dimensional electrophoretic analysis of Corynebacterium glutamicum membrane fraction and surface proteins

An improved protocol for the two-dimensional analysis of proteins of the Corynebacterium glutamicum cytoplasmic membrane fraction is described. By use of increased 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate (CHAPS) concentrations (2-4%) and an optimized electrophoresis protocol, horizontal streaking of proteins of the cytoplasmic membrane fraction was almost completely avoided. More important, in contrast to a previously published method, both a sample tray and IPG-phor isoelectric focusing unit can be used for the in-gel application of proteins. The described protocol was also found to be suitable for hydrophilic cytoplasmic proteins. Additionally, the preparation and analysis of C. glutamicum cell surface proteins is described. Proteins were extracted with lauroyl sarcosinate and 100-120 spots were separated on two-dimensional (2-D) gels in comparison to 18-20 spots observed previously by standard sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). C. glutamicum proteins can now be separated into three distinct fractions resembling different functional units of the bacterial cell.

Aphid transmission of cauliflower mosaic virus requires the viral PIII protein

The open reading frame (ORF) III product (PIII) of cauliflower mosaic virus is necessary for the infection cycle but its role is poorly understood. We have used in vitro protein binding ('far Western') assays to demonstrate that PIII interacts with the cauliflower mosaic virus (CaMV) ORF II product (PII), a known aphid transmission factor. Aphid transmission of purified virions of the PII-defective strain CM4-184 was dependent upon added PII, but complementation was efficient only in the presence of PIII, demonstrating the requirement of PIII for transmission. Deletion mutagenesis mapped the interaction domains of PIII and PII to the 30 N-terminal and 61 C-terminal residues of PIII and PII, respectively. A model for interaction between PIII and PII is proposed on the basis of secondary structure predictions. Finally, a direct correlation between the ability of PIII and PII to interact and aphid transmissibility of the virus was demonstrated by using mutagenized PIII proteins. Taken together, these data argue strongly that PIII is a second 'helper' factor required for CaMV transmission by aphids.

Stitching together RNA tertiary architectures

The powerful explanatory paradigm of molecular biology requiring form to co-evolve with function has again been proven successful when, over the recent two decades, a wealth of biological functions have been uncovered for RNA. Previously considered as a mere mediator of the genetic code, RNA is now acknowledged as a key player in a wide variety of cellular processes. Along with the discovery of novel biological functions of RNA molecules, a number of RNA three-dimensional structures have been solved which beautifully demonstrate the molecular adaptability which allows RNA to participate as a key player in these functions. A distinct repertoire of molecular motifs provides a basis for the assembly of complex RNA tertiary architectures.

Non-Watson-Crick base pairs in RNA-protein recognition

The cellular functions of most RNA molecules involve protein binding, and non-Watson-Crick base pairs are hallmark sites for interactions with proteins. The determination of three-dimensional structures of RNA-peptide and RNA-protein complexes reveals the molecular basis of non-Watson-Crick base-pair recognition.