Computational Design of Novel Allosteric Inhibitors for Plasmodium falciparum DegP

The serine protease, DegP exhibits proteolytic and chaperone activities, essential for cellular protein quality control and normal cell development in eukaryotes. The P. falciparum DegP is essential for the parasite survival and required to combat the oscillating thermal stress conditions during the infection, protein quality checks and protein homeostasis in the extra-cytoplasmic compartments, thereby establishing it as a potential target for drug development against malaria. Previous studies have shown that diisopropyl fluorophosphate (DFP) and the peptide SPMFKGV inhibit E. coli DegP protease activity. To identify novel potential inhibitors specific to PfDegP allosteric and the catalytic binding sites, we performed a high throughput in silico screening using Malaria Box, Pathogen Box, Maybridge library, ChEMBL library and the library of FDA approved compounds. The screening helped identify five best binders that showed high affinity to PfDegP allosteric (T0873, T2823, T2801, {"type":"entrez-protein","attrs":{"text":"RJC02337","term_id":"1480409465","term_text":"RJC02337"}}RJC02337, CD00811) and the catalytic binding site (T0078L, T1524, T2328, BTB11534 and 552691). Further, molecular dynamics simulation analysis revealed {"type":"entrez-protein","attrs":{"text":"RJC02337","term_id":"1480409465","term_text":"RJC02337"}}RJC02337, BTB11534 as the best hits forming a stable complex. WaterMap and electrostatic complementarity were used to evaluate the novel bio-isosteric chemotypes of {"type":"entrez-protein","attrs":{"text":"RJC02337","term_id":"1480409465","term_text":"RJC02337"}}RJC02337, that led to the identification of 231 chemotypes that exhibited better binding affinity. Further analysis of the top 5 chemotypes, based on better binding affinity, revealed that the addition of electron donors like nitrogen and sulphur to the side chains of butanoate group are more favoured than the backbone of butanoate group. In a nutshell, the present study helps identify novel, potent and Plasmodium specific inhibitors, using high throughput in silico screening and bio-isosteric replacement, which may be experimentally validated.     

Crystal Structure of L-Quebrachitol

L-Quebrachitol (1) isolated from the root of Elaeagnus formosana Nakai (Elaeagnaceae) has not been reported before for any species of the genus of Elaeasnus. Its structure was established from spectral data and was completely characterized by single-crystal X-ray analysis. L-Quebrachitol crystallizes in the monoclinic system, space group P2₁, with cell parameters are a = 6.702(4), b = 7.207(4), c = 8.758(5) Å, β = 90.24(5)° and Z = 2.     

The Lamb-dip spectrum of methylcyanide: Precise rotational transition frequencies and improved ground-state rotational parameters

Methylcyanide, CH₃CN, is an important interstellar species, and therefore the accurate knowledge of precise rest frequencies for rotational transitions as well as ground-state rotational and hyperfine constants is needed. In this work the hyperfine structure of the millimeter- and submillimeter-wave spectra of CH₃CN has been further investigated. In addition, accurate THz measurements have been carried out for the first time. Consequently, the present investigation allowed us to provide the most accurate ground state rotational and hyperfine parameters known at the moment for CH₃C¹⁴N. To resolve the hyperfine structure of the rotational transitions observed, the Lamb-dip technique has been exploited. Both frequency-modulated and video-type detections have been employed.     

Surface structures formed by individual adsorption and coadsorption of Mn and Bi on Cu(0 0 1), studied by LEED

We have studied the individual adsorption of Mn and Bi, and their coadsorption on Cu(0 0 1) by low-energy electron diffraction (LEED). For Mn, we have determined the c(2 × 2) structure formed at 300 K, whose structure had been determined by several methods. We reconfirmed by a tensor LEED analysis that it is a substitutional structure and that a previously reported large corrugation (0.30 Å) between substitutional Mn and remaining surface Cu atoms coincides perfectly with the present value. In the individual adsorption of Bi, we have found a c(4 × 2) structure, which is formed by cooling below ∼250 K a surface prepared by Bi deposition of ∼0.25 ML coverage at 300 K where streaky half-order LEED spots appear. The c(4 × 2) structure has been determined by the tensor LEED analysis at 130 K and it is a substitutional structure. In the coadsorption, we found a c(6 × 4) structure, which has been determined by the tensor LEED analysis. It is very similar to the previously determined structure of the c(6 × 4) formed by coadsorption of Mg and Bi, and embedded MnBi₄ clusters are arranged in the top Cu layer instead of MgBi₄. Large lateral displacements of Bi atoms in the c(6 × 4)-(Mn + Bi) suggest that the Mn atoms undergo the size-enhancement caused by their large magnetic moment.     

A study of structural, compositional and optical properties of spray-deposited non-stoichiometric (Zn,Fe)S thin films

Non-stoichiometric ternary chalcogenides (Zn,Fe)S were prepared in the film form by pyrolytic spray deposition technique, using air/nitrogen as the carrier gas. The precursor solution comprised of ZnCl₂, FeCl₂ and thiourea. The depositions were carried out under optimum conditions of experimental parameters viz. carrier gas (air/nitrogen) flow rate, concentration of precursor constituents, nozzle substrate distance and temperature of quartz substrate. The deposited thin films were later sintered in argon at 1073 K for 120 min.The structural, compositional and optical properties of the sintered thin films were studied. X-ray diffraction studies of the thin films indicated the presence of (Zn,Fe)S solid solution with prominent cubic sphalerite phase while surface morphology as determined by scanning electron microscopy (SEM) revealed a granular structure.The chemical composition of the resulting thin films as analyzed by energy dispersive X-ray analysis (EDAX) reflected the composition of the precursor solutions from which the depositions were carried out with Fe at% values ranging from 0.4 up to 33.SEM micrographs of thin films reveal that the grain sizes of the thin films prepared using air as carrier gas and N₂ as carrier gas are in the vicinity of 300 and 150 nm, respectively.The diffuse transmittance measurements for thin films, as a function of wavelength reveal the dependence of direct optical band gap on Fe content and type of phase.     

Study of thermal currents in powder β-spodumene ceramics doped with Cuo, FeO and TiO2

Ternary-phase ceramic system of Li₂O Al₂O₃ 4SiO₂ doped with CuO, FeO and TiO₂ has been prepared and subjected to dc electrical conductivity and thermally stimulated depolarization current (TSDC) measurements as a function of temperature (30-250 °C) and field strength. The electrical conductivity results are explained by assuming both ionic and electronic conduction mechanisms coexist with different contributions over the whole temperature range of experiments. TSDC spectra have been found to be characterized by a broad intense relaxation peak, which can be attributed to an ionic charge polarization. The broad relaxation transitions are apparently a result of the nonuniform nature of this process. Activation energies are calculated for both dc electrical conductivity and TSDC according to Arrhenius equation and initial rise method, respectively.     

Structures and stability of Al<Subscript><Emphasis Type="Bold">7</Emphasis></Subscript>C and Al<Subscript><Emphasis Type="Bold">7</Emphasis></Subscript>N clusters

We report results of the atomic and electronic structures of Al₇C cluster using ab initio molecular dynamics with ultrasoft pseudopotentials and generalized gradient approximation. The lowest energy structure is found to be the one in which carbon atom occupies an interstitial position in Al₇ cluster. The electronic structure shows that the recent observation [Chem. Phys. Lett. 316, 31 (2000)] of magic behavior of Al₇C^- cluster is due to a large highest occupied and lowest unoccupied molecular orbital (HOMO-LUMO) gap which makes Al₇C^- chemically inert. These results have further led us to the finding of a new neutral magic cluster Al₇N which has the same number of valence electrons as in Al₇C^- and a large HOMO-LUMO gap of 1.99 eV. Further, calculations have been carried out on (Al₇N)₂ to study interaction between magic clusters. Received 28 July 2001     

Electrical behavior of the Au/MoS2 interface studied by light emission induced by scanning tunneling microscopy

Light emitted in the tunneling junction of a scanning tunneling microscope has been used to establish the electrical characteristics of nanojunctions made of Au islands deposited on flat MoS₂ surfaces. It is shown that these characteristics are those of rectifying contacts when the gold islands are isolated and that they evolve toward those of ohmic contacts when the island density increases. It is observed that the rectifying behavior also evolves over time as on infinite metal/semiconductor contacts. Using the STM tip, single gold islands can be manipulated on the MoS₂ surface so that their electrical behavior can be changed depending on their position with regard to the other islands.     

The measurement of subcritical electroconvection

Under idealized conditions, electroconvection in a nematic liquid crystal sets in at a well-defined threshold of the driving ac voltage. Fluctuating convection rolls of a small amplitude below that threshold have been observed recently. The measurement of the amplitude of these fluctuations is described in detail in this paper. It is based on averaging the light intensity signals using the structure function and a quantitative analysis of the light deflection.