G-quadruplex DNA motifs in the malaria parasite Plasmodium falciparum and their potential as novel antimalarial drug targets

G-quadruplexes are DNA or RNA secondary structures that can be formed from guanine-rich nucleic acids. These four-stranded structures, composed of stacked quartets of guanine bases, can be highly stable and have been demonstrated to occur in vivo in the DNA of human cells and other systems, where they play important biological roles, influencing processes such as telomere maintenance, DNA replication and transcription, or, in the case of RNA G-quadruplexes, RNA translation and processing. We report for the first time that DNA G-quadruplexes can be detected in the nuclei of the malaria parasite Plasmodium falciparum, which has one of the most A/T-biased genomes sequenced and therefore possesses few guanine-rich sequences with the potential to form G-quadruplexes. We show that despite this paucity of putative G-quadruplex-forming sequences, P. falciparum parasites are sensitive to several G-quadruplex-stabilizing drugs, including quarfloxin, which previously reached phase 2 clinical trials as an anticancer drug. Quarfloxin has a rapid initial rate of kill and is active against ring stages as well as replicative stages of intraerythrocytic development. We show that several G-quadruplex-stabilizing drugs, including quarfloxin, can suppress the transcription of a G-quadruplex-containing reporter gene in P. falciparum but that quarfloxin does not appear to disrupt the transcription of rRNAs, which was proposed as its mode of action in both human cells and trypanosomes. These data suggest that quarfloxin has potential for repositioning as an antimalarial with a novel mode of action. Furthermore, G-quadruplex biology in P. falciparum may present a target for development of other new antimalarial drugs

Solution structures of the Bacillus cereus metallo-β-lactamase BcII and its complex with the broad spectrum inhibitor R-thiomandelic acid

Metallo-β-lactamases, enzymes which inactivate β-lactam antibiotics, are of increasing biological and clinical significance as a source of antibiotic resistance in pathogenic bacteria. In the present study we describe the high-resolution solution NMR structures of the Bacillus cereus metallo-β-lactamase BcII and of its complex with R-thiomandelic acid, a broad-spectrum inhibitor of metallo-β-lactamases. This is the first reported solution structure of any metallo-β-lactamase. There are differences between the solution structure of the free enzyme and previously reported crystal structures in the loops flanking the active site, which are important for substrate and inhibitor binding and catalysis. The binding of R-thiomandelic acid and the roles of active-site residues are defined in detail. Changes in the enzyme structure upon inhibitor binding clarify the role of the mobile β3–β4 loop. Comparisons with other metallo-β-lactamases highlight the roles of individual amino-acid residues in the active site and the β3–β4 loop in inhibitor binding and provide information on the basis of structure–activity relationships among metallo-β-lactamase inhibitors

Enumerating Pathways of Proton Abstraction Based on a Spatial and Electrostatic Analysis of Residues in the Catalytic Site

The pathways of proton abstraction (PA), a key aspect of most catalytic reactions, is often controversial and highly debated. Ultrahigh-resolution diffraction studies, molecular dynamics, quantum mechanics and molecular mechanic simulations are often adopted to gain insights in the PA mechanisms in enzymes. These methods require expertise and effort to setup and can be computationally intensive. We present a push button methodology – Proton abstraction Simulation (PRISM) – to enumerate the possible pathways of PA in a protein with known 3D structure based on the spatial and electrostatic properties of residues in the proximity of a given nucleophilic residue. Proton movements are evaluated in the vicinity of this nucleophilic residue based on distances, potential differences, spatial channels and characteristics of the individual residues (polarity, acidic, basic, etc). Modulating these parameters eliminates their empirical nature and also might reveal pathways that originate from conformational changes. We have validated our method using serine proteases and concurred with the dichotomy in PA in Class A β-lactamases, both of which are hydrolases. The PA mechanism in a transferase has also been corroborated. The source code is made available at www.sanchak.com/prism

Ligand Binding Study of Human PEBP1/RKIP: Interaction with Nucleotides and Raf-1 Peptides Evidenced by NMR and Mass Spectrometry

Background Human Phosphatidylethanolamine binding protein 1 (hPEBP1) also known as Raf kinase inhibitory protein (RKIP), affects various cellular processes, and is implicated in metastasis formation and Alzheimer's disease. Human PEBP1 has also been shown to inhibit the Raf/MEK/ERK pathway. Numerous reports concern various mammalian PEBP1 binding ligands. However, since PEBP1 proteins from many different species were investigated, drawing general conclusions regarding human PEBP1 binding properties is rather difficult. Moreover, the binding site of Raf-1 on hPEBP1 is still unknown. Methods/Findings In the present study, we investigated human PEBP1 by NMR to determine the binding site of four different ligands: GTP, FMN, and one Raf-1 peptide in tri-phosphorylated and non-phosphorylated forms. The study was carried out by NMR in near physiological conditions, allowing for the identification of the binding site and the determination of the affinity constants KD for different ligands. Native mass spectrometry was used as an alternative method for measuring KD values. Conclusions/Significance Our study demonstrates and/or confirms the binding of hPEBP1 to the four studied ligands. All of them bind to the same region centered on the conserved ligand-binding pocket of hPEBP1. Although the affinities for GTP and FMN decrease as pH, salt concentration and temperature increase from pH 6.5/NaCl 0 mM/20°C to pH 7.5/NaCl 100 mM/30°C, both ligands clearly do bind under conditions similar to what is found in cells regarding pH, salt concentration and temperature. In addition, our work confirms that residues in the vicinity of the pocket rather than those within the pocket seem to be required for interaction with Raf-1.METASU

Palynological and chemical volatile components of tipically autumnal honeys of the western Mediterranean

[EN] Twenty-five samples of autumnal honeys from the western Mediterranean (Mallorca and Eivissa, Balearic Islands) were examined for pollen content (qualitative and quantitative melissopalynological analysis), moisture, electrical conductivity, colour, sensorial qualities and volatile components. Quantitative analysis showed that the honey contained Maurizio's Class II: 64%, Class III: 28%, Class IV: 4% and Class V: 4%. Fifty-four pollen types, with an average number of 16.68 per sample, were identified, belonging to 29 botanical families. Only two taxa (Ceratonia siliqua and Erica multiflora) were found in all samples. Seventeen samples were unifloral (68%) - ten (40%) of C. siliqua, six (24%) of E. multiflora and one (4%) of Hedera helix. All honeys have a low honeydew index (<?0.09%), while the values for electrical conductivity and water content were high. The major honey volatile components are: cis- and trans-linalool oxides (64.2%) and hotrienol (10.4%) for the carob (C. siliqua) and trans-linalool oxide (13.4%), p-menthane-1,8-diol (11.1%), safranal (9.7%), limonene (5,4%), -pinene (3.7%) and oxoisophorone (3.4%) for the winter heather (E. multiflora).The authors would like to extend their gratitude to the Mallorca Rural 'Leader plus' programme and the beekeepers of Mallorca and Eivissa for their support and friendly collaboration. The authors also thank an anonymous reviewer for useful comments and suggestions on an earlier version of the manuscript.Boi, M.; Llorens Molina, JA.; Cortés, L.; Lladó, G.; Llorens, L. (2013). Palynological and chemical volatile components of tipically autumnal honeys of the western Mediterranean. Grana. 52(2):93-105. doi:10.1080/00173134.2012.744774S93105522Andrade, P. B., Amaral, M. T., Isabel, P., Carvalho, J. C. M. F., Seabra, R. M., & Proença da Cunha, A. (1999). 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A variety of roles for versatile zinc in metallo-b-lactamases

Metallo-b-lactamases are important as a major source of resistance of pathogenic bacteria to the widely used b-lactam antibiotics. They show considerable diversity in terms of sequence and are grouped into three subclasses, B1, B2 and B3, which share a common overall fold. In each case the active enzyme has binding sites for two zinc ions in close proximity, although the amino-acid residues which coordinate the metals vary from one subclass to another. In subclasses B1 and B3, there has been controversy about whether both zinc ions are required for activity, but the most recent evidence indicates that there is positive cooperativity in zinc binding and that the catalytically relevant species is the di-zinc enzyme. Subclass B2 enzymes, on the other hand, are active in the mono-zinc state and are inhibited by the binding of a second zinc ion. Evidence for the importance of the zinc ions in substrate binding has come from structures of product complexes which indicate that the b-lactam core binds to subclass B1 and B3 enzymes in a rather consistent fashion, interactions with the zinc ions being centrally important. The zinc ions play key roles in the catalytic mechanism, including facilitating nucleophilic attack on the amide carbonyl by the zinc-bound hydroxide ion, stabilising the anionic tetrahedral intermediate and coordinating the departing amine nitrogen

Complete 1H, 15N and 13C resonance assignments of Bacillus cereus metallo-b-lactamase and its complex with the inhibitor R-thiomandelic acid

b-Lactamases inactivate b-lactam antibiotics by hydrolysis of their endocyclic b-lactam bond and are a major cause of antibiotic resistance in pathogenic bacteria. The zinc dependent metallo-b-lactamase enzymes are of particular concern since they are located on highly transmissible plasmids and have a broad spectrum of activity against almost all b-lactam antibiotics. We present here essentially complete ([96 %) backbone and sidechain sequence-specific NMR resonance assignments for the Bacillus cereus subclass B1 metallo-b-lactamase, BcII, and for its complex with R-thiomandelic acid, a broad spectrum inhibitor of metallo-b-lactamases. These assignments have been used as the basis for determination of the solution structures of the enzyme and its inhibitor complex and can also be used in a rapid screen for other metallo-b-lactamase inhibitors