Structural basis for the inhibition of the essential Plasmodium falciparum M1 neutral aminopeptidase

Plasmodium falciparum parasites are responsible for the major global disease malaria, which results in > 2 million deaths each year. With the rise of drug-resistant malarial parasites, novel drug targets and lead compounds are urgently required for the development of new therapeutic strategies. Here, we address this important problem by targeting the malarial neutral aminopeptidases that are involved in the terminal stages of hemoglobin digestion and essential for the provision of amino acids used for parasite growth and development within the erythrocyte. We characterize the structure and substrate specificity of one such aminopeptidase, PfA-M1, a validated drug target. The X-ray crystal structure of PfA-M1 alone and in complex with the generic inhibitor, bestatin, and a phosphinate dipeptide analogue with potent in vitro and in vivo antimalarial activity, hPheP[CH2] Phe, reveals features within the protease active site that are critical to its function as an aminopeptidase and can be exploited for drug development. These results set the groundwork for the development of antimalarial therapeutics that target the neutral aminopeptidases of the parasite.

Structure of the Plasmodium falciparum M17 aminopeptidase and significance for the design of drugs targeting the neutral exopeptidases

Current therapeutics and prophylactics for malaria are under severe challenge as a result of the rapid emergence of drug-resistant parasites. The human malaria parasite Plasmodium falciparum expresses two neutral aminopeptidases, PfA-M1 and PfA-M17, which function in regulating the intracellular pool of amino acids required for growth and development inside the red blood cell. These enzymes are essential for parasite viability and are validated therapeutic targets. We previously reported the x-ray crystal structure of the monomeric PfA-M1 and proposed a mechanism for substrate entry and free amino acid release from the active site. Here, we present the x-ray crystal structure of the hexameric leucine aminopeptidase, PfA-M17, alone and in complex with two inhibitors with antimalarial activity. The six active sites of the PfA-M17 hexamer are arranged in a disc-like fashion so that they are orientated inwards to form a central catalytic cavity; flexible loops that sit at each of the six entrances to the catalytic cavern function to regulate substrate access. In stark contrast to PfA-M1, PfA-M17 has a narrow and hydrophobic primary specificity pocket which accounts for its highly restricted substrate specificity. We also explicate the essential roles for the metal-binding centers in these enzymes (two in PfA-M17 and one in PfA-M1) in both substrate and drug binding. Our detailed understanding of the PfA-M1 and PfA- M17 active sites now permits a rational approach in the development of a unique class of two-target and/or combination antimalarial therapy.

A STUDY OF CARBON-MONOXIDE AND NEUTRAL CARBON IN THE S106 MOLECULAR CORE

Maps are presented of J=2-1 and J=3-2 (CO)-O-18 emission from the molecular environment of the bipolar nebula S106, together with complementary observations of the P-3(1)-P-3(0), C I emission. Line splitting observed extensively over the E molecular cloud suggests that it is best explained as the expanding remnant of a thick toroid surrounding the optical lobes. The poor correlation between the observed molecular line emission and dust continuum emission in the E cloud is probably due to a large temperature gradient. Strong C I emission from the protostellar candidate S106 FIR suggests the nearby presence of a powerful source of far-UV radiation, whose energy supply is unlikely to arise from gravitational contraction of a protostar. It is probable that this source is the star S106 LR, which also heats S106 FIR. There is evidence, in both C I and (CO)-O-18, for a predominantly blueshifted outflow from S106 IR, best interpreted as a stellar wind-driven shock into the toroidal remnant. (CO)-O-18 and (CO)-C-13 appear to be depleted, relative to canonical values for their abundances, in S106 FIR, despite its high optical extinction, which should discourage selective photodissociation. Elsewhere in the cloud the C I line profiles show a resemblance to those of (CO)-O-18, with intensity equivalent to a few photodissociation regions (PDRs) along the line of sight.

THE EFFECT OF RAPID NEUTRAL-NEUTRAL REACTIONS ON CHEMICAL-MODELS OF DENSE INTERSTELLAR CLOUDS

Recent experiments on rapid neutral-neutral reactions involving the radical CN at low temperature and the neutral C atom at room temperature suggest that atom-neutral and radical-neutral reactions may be generally more rapid at low temperature than hitherto thought. We have included a variety of rapid neutral-neutral reactions in our gas-phase chemical models of quiescent, dense interstellar clouds. We find the calculated abundances of many molecules to be greatly changed from previous values. In particular, the peak 'early-time' abundances of organic molecules are reduced.

Energy levels, wavefunction compositions and electric dipole transitions in neutral Ca

A configuration-interaction approach, based on the use of B-spline basis sets combined with a model potential including monoelectronic and dielectronic core polarization effects, is employed to calculate term energies and wavefunctions for neutral Ca. Results are reported for singlet and triplet bound states, and some quasi-bound states above the lowest ionization limit, with angular momentum up to L = 4. Comparison with experiment and with other theoretical results shows that this method yields the most accurate energy values for neutral Ca obtained to date. Wavefunction compositions, necessary for labelling the levels, and the effects of semi-empirical polarization potentials on the wavefunctions are discussed, as are some recent identifications of doubly-excited states. It is shown that taking into account dielectronic core polarization changes the energies of the lowest terms in Ca significantly, in general by a few hundred cm(-1), the effect decreasing rapidly for the higher bound states. For Rydberg states with n approximate to 7 the accuracy of the results is often better than a few cm(-1). For series members (or perturbers) with a pronounced 3d character the error can reach 150 cm(-1). The wavefunctions are used to calculate oscillator strengths and lifetimes for a number of terms and these are compared with existing measurements. The agreement is good but points to a need for improved measurements.

Electron paramagnetic resonance studies of the neutral nitrogen vacancy in diamond

Despite the numerous experimental and theoretical studies on the negatively charged nitrogen vacancy center (NV-) in diamond and the predictions that the neutral nitrogen vacancy center (NV0) should have an S=1/2 ground state, NV0 has not previously been detected by electron paramagnetic resonance (EPR). We report new EPR data on a trigonal nitrogen-containing defect in diamond with an S=3/2 excited state populated via optical excitation. Analysis of the spin Hamiltonian parameters and the wavelength dependence of the optical excitation leads to assignment of this S=3/2 state to the (4)A(2) excited state of NV0. This identification, together with an examination of the electronic structure of the NV centers in diamond, provides a plausible explanation for the lack of observation (to date) of an EPR signal from the NV0 ground state.

Comparative performances of birnessite and cryptomelane MnO as electrode material in neutral aqueous lithium salt for supercapacitor application

Na-doped Birnessite-type manganese oxide (d-MnO) has been synthesized using the chemical method and characterized through X-ray diffraction and SEM, showing the lamellar structure and high crystal structure. A comparative study of the electrochemical performances of this material with those of the commercial Cryptomelane-type MnO has then been undertaken in ten neutral aqueous electrolytes for supercapacitor applications. Aqueous electrolytes, containing a lithium salt, LiX (where X = SO , NO, CHCO , CHSO, ClO , CHCO, TFSI, Beti, BOB, or Lact), have been first prepared under neutral pH conditions to reach the salt concentration, providing the maximum in conductivity. Their transport properties are then investigated through conductivities, viscosities, and self-diffusion coefficient measurements. Second, the thermal behaviors of these electrolytic aqueous solutions are then evaluated by using a differential scanning calorimeter from (213.15 to 473.15) K in order to access their liquid range temperatures. Cyclic voltammograms (CV) in three electrode configurations are thereafter investigated using Na Birnessite and Cryptomelane as working electrode material from (-0.05 to 1.5) V versus Ag/AgCl at various sweep rates from (2 to 100) mV·s. According to anion nature/structure and manganese oxide material type, different CV responses are observed, presenting a pure capacitive profile for Beti or CH CO and an additional pseudocapacitive signal for the smallest anions, such as ClO and NO . The capacitances, energies, and efficiencies are finally calculated. These results indicate clearly that electrolytes based on a mineral lithium salt under neutral pH condition and high salt concentration (up to 5 mol·L) have better electrochemical performances than organic ones, up to 1.4 V with good material stability and capacity retention. The relationship between transport properties, electrostatic and steric hindrance considerations of hydrated ions, and their electrochemical performances is discussed in order to understand further the lithium intercalation-deintercalation processes in the lamellar or tunnel structure of investigated MnO. © 2013 American Chemical Society.

Fragmentation of Neutral Amino Acids and Small Peptides by Intense, Femtosecond Laser Pulses

High power femtosecond laser pulses have unique properties that could lead to their application as ionization or activation sources in mass spectrometry. By concentrating many photons into pulse lengths approaching the timescales associated with atomic motion, very strong electric field strengths are generated, which can efficiently ionize and fragment molecules without the need for resonant absorption. However, the complex interaction between these pulses and biomolecular species is not well understood. To address this issue, we have studied the interaction of intense, femtosecond pulses with a number of amino acids and small peptides. Unlike previous studies, we have used neutral forms of these molecular targets, which allowed us to investigate dissociation of radical cations without the spectra being complicated by the action of mobile protons. We found fragmentation was dominated by fast, radical-initiated dissociation close to the charge site generated by the initial ionization or from subsequent ultrafast migration of this charge. Fragments with lower yields, which are useful for structural determinations, were also observed and attributed to radical migration caused by hydrogen atom transfer within the molecule.

Thomson spectrometer-microchannel plate assembly calibration for MeV-range positive and negative ions, and neutral atoms

We report on the absolute calibration of a microchannel plate (MCP) detector, used in conjunction with a Thomson parabola spectrometer. The calibration delivers the relation between a registered count numbers in the CCD camera (on which the MCP phosphor screen is imaged) and the number of ions incident on MCP. The particle response of the MCP is evaluated for positive, negative, and neutral particles at energies below 1 MeV. As the response of MCP depends on the energy and the species of the ions, the calibration is fundamental for the correct interpretation of the experimental results. The calibration method and arrangement exploits the unique emission symmetry of a specific source of fast ions and atoms driven by a high power laser.

Neutral Genomic Microevolution of a Recently Emerged Pathogen, Salmonella enterica Serovar Agona

Salmonella enterica serovar Agona has caused multiple food-borne outbreaks of gastroenteritis since it was first isolated in 1952. We analyzed the genomes of 73 isolates from global sources, comparing five distinct outbreaks with sporadic infections as well as food contamination and the environment. Agona consists of three lineages with minimal mutational diversity: only 846 single nucleotide polymorphisms (SNPs) have accumulated in the non-repetitive, core genome since Agona evolved in 1932 and subsequently underwent a major population expansion in the 1960s. Homologous recombination with other serovars of S. enterica imported 42 recombinational tracts (360 kb) in 5/143 nodes within the genealogy, which resulted in 3,164 additional SNPs. In contrast to this paucity of genetic diversity, Agona is highly diverse according to pulsed-field gel electrophoresis (PFGE), which is used to assign isolates to outbreaks. PFGE diversity reflects a highly dynamic accessory genome associated with the gain or loss (indels) of 51 bacteriophages, 10 plasmids, and 6 integrative conjugational elements (ICE/IMEs), but did not correlate uniquely with outbreaks. Unlike the core genome, indels occurred repeatedly in independent nodes (homoplasies), resulting in inaccurate PFGE genealogies. The accessory genome contained only few cargo genes relevant to infection, other than antibiotic resistance. Thus, most of the genetic diversity within this recently emerged pathogen reflects changes in the accessory genome, or is due to recombination, but these changes seemed to reflect neutral processes rather than Darwinian selection. Each outbreak was caused by an independent clade, without universal, outbreak-associated genomic features, and none of the variable genes in the pan-genome seemed to be associated with an ability to cause outbreaks. © 2013 Achtman et al