Discovery of novel inhibitors for <Emphasis Type="Italic">Leishmania</Emphasis> nucleoside diphosphatase kinase (NDK) based on its structural and functional characterization

Nucleoside diphosphate kinases (NDKs) are ubiquitous enzymes that catalyze the transfer of the γ-phosphate moiety from an NTP donor to an NDP acceptor, crucial for maintaining the cellular level of nucleoside triphosphates (NTPs). The inability of trypanosomatids to synthesize purines de novo and their dependence on the salvage pathway makes NDK an attractive target to develop drugs for the diseases they cause. Here we report the discovery of novel inhibitors for Leishmania NDK based on the structural and functional characterization of purified recombinant NDK from Leishmania amazonensis. Recombinant LaNDK possesses auto-phosphorylation, phosphotransferase and kinase activities with Histidine 117 playing an essential role. LaNDK crystals were grown by hanging drop vapour diffusion method in a solution containing 18% PEG-MME 500, 100 mM Bis-Tris propane pH 6.0 and 50 mM MgCl₂. It belongs to the hexagonal space group P6₃22 with unit cell parameters a?=?b?=?115.18, c?=?62.18 Å and α?=?β?=?90°, γ?=?120°. The structure solved by molecular replacement methods was refined to crystallographic R-factor and R_free values of 22.54 and 26.52%, respectively. Molecular docking and dynamics simulation-based virtual screening identified putative binding compounds. Protein inhibition studies of selected hits identified five inhibitors effective at micromolar concentrations. One of the compounds showed ~45% inhibition of Leishmania promastigotes proliferation. Analysis of inhibitor-NDK complexes reveals the mode of their binding, facilitating design of new compounds for optimization of activities as drugs against leishmaniasis.     

Trehalose-6-Phosphate as a Potential Lead Candidate for the Development of Tps1 Inhibitors: Insights from the Trehalose Biosynthesis Pathway in Diverse Yeast Species

In some pathogens, trehalose biosynthesis is induced in response to stress as a protection mechanism. This pathway is an attractive target for antimicrobials as neither the enzymes, Tps1, and Tps2, nor is trehalose present in humans. Accumulation of T6P in Candida albicans, achieved by deletion of TPS2, resulted in strong reduction of fungal virulence. In this work, the effect of T6P on Tps1 activity was evaluated. Saccharomyces cerevisiae, C. albicans, and Candida tropicalis were used as experimental models. As expected, a heat stress induced both trehalose accumulation and increased Tps1 activity. However, the addition of 125 μM T6P to extracts obtained from stressed cells totally abolished or reduced in 50 and 60 % the induction of Tps1 activity in S. cerevisiae, C. tropicalis, and C. albicans, respectively. According to our results, T6P is an uncompetitive inhibitor of S. cerevisiae Tps1. This kind of inhibitor is able to decrease the rate of reaction to zero at increased concentrations. Based on the similarities found in sequence and function between Tps1 of S. cerevisiae and some pathogens and on the inhibitory effect of T6P on Tps1 activity observed in vitro, novel drugs can be developed for the treatment of infectious diseases caused by organisms whose infectivity and survival on the host depend on trehalose.     

Density,Viscosity, and Glass Transition of an Ethylenediamine–Ethylene Glycol Binary System

Densities ρ and viscosities η were measured for the binary mixtures of ethylenediamine (EDA) and ethylene glycol (EG) in the temperature range 288.15–323.15 K for ρ and at 273.15–323.15 K for η, both of which are broader temperature ranges than those reported previously. The value of ρ monotonously decreases against the mole fraction of EDA, x _EDA, and increasing temperature. The concentration dependence of η exhibits a maximum in the intermediate concentration range at all temperatures measured. The glass transition temperature, T _g, for samples with x _EDA < 0.7 was measured using differential scanning calorimetry. The measured T _g values show a peak in the intermediate concentration range, which is a behavior similar to that of η; however, the peak concentrations for η and T _g did not precisely align because of a deviation in the maximum hydrogen-bond density. The partial molar volumes for EDA and EG and the thermal expansivities, α, were obtained from ρ. Results in the present study are discussed in terms of the extensively increasing hydrogen-bond density for polyamine–polyhydric alcohol systems.     

Modeling the Growth of Archaeon <Emphasis Type="Italic">Halobacterium halobium</Emphasis> Affected by Temperature and Light

The objective of this study was to develop sigmoidal models, including three-parameter (Quadratic, Logistic, and Gompertz) and four-parameter models (Schnute and Richards) to simulate the growth of archaeon Halobacterium halobium affected by temperature and light. The models were statistically compared by using t test and F test. In the t test, confidence bounds for parameters were used to distinguish among models. For the F test, the lack of fit of the models was compared with the prediction error. The Gompertz model was 100 % accepted by the t test and 97 % accepted by the F test when the temperature effects were considered. Results also indicated that the Gompertz model was 94 % accepted by the F test when the growth of H. halobium was studied under varying light intensities. Thus, the Gompertz model was considered the best among the models studied to describe the growth of H. halobium affected by temperature or light. In addition, the biological growth parameters, including specific growth rate, lag time, and asymptote changes under Gompertz modeling, were evaluated.     

Phylogenetic Analysis and Biological Evaluation of Marine Endophytic Fungi Derived from Red Sea Sponge <Emphasis Type="Italic">Hyrtios erectus</Emphasis>

Forty-four endophytic fungal isolates obtained from marine sponge, Hyrtios erectus, were evaluated and screened for their hydrolase activities. Most of the isolates were found to be prolific producers of hydrolytic enzymes. Only 11 isolates exhibited maximum cellular contents of lipids, rhamnolipids, and protein in the fungal isolates under the isolation numbers MERVA5, MERVA22, MERVA25, MERVA29, MERVA32, MERVA34, MERV36, MERVA39, MERVA42, MERVA43, and MERVA44. These isolate extracts exhibit the highest reducing activities against carbohydrate-metabolizing enzymes including α-amylase, α-glucosidase, β-glucosidase, β-glucuronidase, and tyrosinase. Consequently, based on morphological and cultural criteria, as well as sequence information and phylogenetic analysis, these isolates could be identified and designated as Penicillium brevicombactum MERVA5, Arthrinium arundinis MERVA22, Diaporthe rudis MERVA25, Aspergillus versicolor MERVA29, Auxarthron alboluteum MERVA32, Dothiorella sarmentorum MERVA34, Lophiostoma sp. MERVA36, Fusarium oxysporum MERVA39, Penicillium chrysogenum MERVA42, Penicillium polonicum MERVA43, and Trichoderma harzianum MERVA44. The endophytic fungal species, D. rudis MERVA25, P. polonicum MERVA43, Lophiostoma sp. MERVA36, A. alboluteum MERVA32, T. harzianum MERVA44, F. oxysporum MERVA39, A. versicolor MERVA29, and P. chrysogenum MERVA42 extracts, showed significant hepatitis C virus (HCV) inhibition. Moreover, D. sarmentorum MERVA34, P. polonicum MERVA43, and T. harzianum MERVA44 extracts have the highest antitumor activity against human hepatocellular carcinoma cells (HepG2).     

Substrate specificity and function of acetylpolyamine amidohydrolases from <Emphasis Type="Italic">Pseudomonas aeruginosa</Emphasis>

Background

Pseudomonas aeruginosa, a Gram-negative, aerobic coccobacillus bacterium is an opportunistic human pathogen and worldwide the fourth most common cause of hospital-acquired infections which are often high mortality such as ventilator-associated pneumoniae. The polyamine metabolism of P. aeruginosa and particularly the deacetylation of acetylpolyamines has been little studied up to now. Results with other bacterial pathogens e.g., Y. pestis suggest that polyamines may be involved in the formation of biofilms or confer resistance against certain antibiotics.

Results

To elucidate the role of acetylpolyamines and their enzymatic deacetylation in more detail, all three putative acetylpolyamine amidohydrolases (APAHs) from P. aeruginosa have been expressed in enzymatic active form. The APAHs PA0321 and PA1409 are shown to be true polyamine deacetylases, whereas PA3774 is not able to deacetylate acetylated polyamines. Every APAH can hydrolyze trifluoroacetylated lysine-derivatives, but only PA1409 and much more efficiently PA3774 can also process the plain acetylated lysine substrate. P. aeruginosa is able to utilize acetylcadaverine and acetylputrescine as a carbon source under glucose starvation. If either the PA0321 or the PA1409 but not the PA3774 gene is disrupted, the growth of P. aeruginosa is reduced and delayed. In addition, we were able to show that the APAH inhibitors SAHA and SATFMK induce biofilm formation in both PA14 and PAO1 wildtype strains.

Conclusions

P. aeruginosa has two functional APAHs, PA0321 and PA1409 which enable the utilization of acetylpolyamines for the metabolism of P. aeruginosa. In contrast, the physiological role of the predicted APAH, PA3774, remains to be elucidated. Its ability to deacetylate synthetic acetylated lysine substrates points to a protein deacetylation functionality with yet unknown substrates.

     

Molecular dynamics simulation of the structure and thermodynamic properties of liquid rubidium at pressures of up to 10 GPa and temperatures of up to 3500 K

The models of rubidium at temperatures of up to 3500 K, degrees of compression of up to Y = V/V₀ = 0.3, and pressures of up to 32 GPa were constructed by molecular dynamics (MD) using the interparticle potential ЕАМ. The thermodynamic properties of the MD models agree satisfactorily with experiment in the range of parameters under study at rubidium densities higher than 0.86 g/cm³. The behavior of the models in the range of the van der Waals loop was analyzed; the calculated critical temperature of rubidium T_c is ～2250 ± 25 K, density ～0.41 g/cm³, pressure ～0.019 GPa, and compressibility factor Z = pV/RT ≈ 0.137. The states with the unity factor Z = 1 were observed at pressures of up to 0.30 GPa (at ～3000 K); the temperature dependence of the density of the models with Z = 1 is nearly linear, and the Boyle temperature is T_B ≈ 10160 K. The ratio T_c/T_B = 0.221 is close to this value for cesium (0.23) and mercury (0.276). In the temperature and pressure ranges under study, the inversion of the Joule–Thomson coefficient did not take place, but should be observed at pressures of ?0.3 GPa and elevated temperatures. It was found that the diffusion coefficient D(T) dependences do not straighten in the usually used coordinates within wide temperature ranges. It was concluded that the structure of the liquid smoothly changes when the rubidium models are compressed and this reveals in the change of the degree of asymmetry of the first peak of the radial distribution function.     

The use of recurrent equations in chromatography

Recurrent equations A(x + k) = aA(x) + b were shown to be applicable to the approximation not only of virtually arbitrary properties of organic compounds (A) in homologous series (A = n _C, k = 1 or 2) but also of the dependences of chromatographic retention parameters on the number of carbon atoms in homologue molecules (A = t _R). The same equations described the temperature dependences of retention times of arbitrary compounds under isothermal separation conditions in gas chromatography (x = T, k = ΔT = const) and the dependences of retention times on the concentration of an organic solvent as an eluent component (x = C, k = ΔC = const) under isocratic separation conditions in high performance liquid chromatography.     

Molecular dynamic studies of amyloid-beta interactions with curcumin and Cu<Superscript>2+</Superscript> ions

Amyloid-beta (Aβ) peptide readily forms aggregates that are associated with Alzheimer’s disease. Transition metals play a key role in this process. Recently, it has been shown that curcumin (CUA), a polyphenolic phytochemical, inhibits the aggregation of Aβ peptide. However, interactions of Aβ peptide with metal ions or CUA are not entirely clear. In this work, molecular dynamics (MD) simulations were carried out to clear the nature of interactions between the 42-residue Aβ peptide (Aβ-42) and Cu²⁺ ions and CUA. Altogether nine different models were investigated, and more than 2 µs of the simulation data were analyzed. The models represent the possible modes of arrangement between Aβ-42 and Cu²⁺ ions and CUA, respectively, and were used to shed light on the Aβ-42 conformational behavior in the presence of Cu²⁺ ions and CUA molecules. Obtained data clearly showed that the presence of a CUA molecule or a higher concentration of copper ions significantly affect the conformational behavior of Aβ-42. Calculations showed that the change of the His13 protonation state (Aβ(H13δ)-Cu²⁺, Aβ(H13δ)-Cu²⁺ -CUA models) leads to higher occurrence of the Asp23-Lys28 salt bridge. Analyzes of trajectories revealed that C-terminal β-sheet structures occurred significantly less frequently, and CUA promoted the stabilization of the α-helical structure. Further, calculations of the Aβ-42 complex with CUA and Cu²⁺ ions showed that CUA can chelate the Cu²⁺ ion and directly interact with Aβ, which may explain why CUA acts as an inhibitor of Aβ aggregation.     

The response electron–electron repulsion energy and energy component analysis in CC/MBPT methods

Molecular properties are computed as responses to perturbations (energy derivatives) in coupled-cluster (CC)/many-body perturbation theory (MBPT) models. Here, the CC/MBPT energy derivative with respect to a general two-electron (2-e) perturbation is assembled from gradient theory for 2-e property evaluation, including the electron repulsion energy. The correlation energy (?E) is shown to be the sum of response kinetic (?T), electron–nuclear attraction (?V), and electron repulsion (?V _ee ) energies. Thus, evaluation of total V _ee for energy component analysis is simple: For total energy (E), total 1-e responses T and V, and nuclear–nuclear repulsion energy (V _NN ), V _ee  = E ? V _NN  ? T ? V is the true 2-e response value. Component energy analysis is illustrated in an assessment of steric repulsion in ethane’s rotational barrier. Earlier SCF-based results (Bader et al. in J Am Chem Soc 112:6530, 1990) are corroborated: The higher-energy eclipsed geometry is favored versus staggered in the two repulsion energies (V _NN and V _ee ), while decisively disfavored in electron–nuclear attraction energy (V). Our best quality calculations (CCSD/cc-pVQZ) attain practical Virial Theorem compliance (i.e., agreement among the kinetic energy, potential energy, and total energy representations) in assigning 2.70 ± 0.06 to the barrier height; ?195.80 kcal/mol is assigned to the drop in “steric” repulsion upon going to the eclipsed geometry. Steric repulsion is not responsible for any fraction of the ~3 kcal/mol barrier.     

Thermal polymerization of styrene: New data on the conversion dependence of the initiation rate

With the aid of new acceptors of free radicals usable at high temperatures (T > 100°C), the rate of initiation w _i has been measured experimentally for the thermal polymerization of styrene at 122.5°C in a wide range of conversions C = 0–80%. It has been shown that the value of w _i tends to increase in the course of polymerization transformation in agreement with the w _i = f(C) relationship calculated from the kinetic data on the thermal polymerization of styrene in the absence of counters of free radicals. Hypothetical reasons for this non-trivial tendency have been formulated. The experimental dependence w _i = f(C) has been measured for the first time and has been invoked to refine currently available mathematical models for the thermal polymerization of styrene that assume that w _i remains invariable in the course of polymerization transformation.     

Alkylation of 2-(methylsulfanyl)-6-polyfluoroalkylpyrimidin-4(3<Emphasis Type="Italic">H</Emphasis>)-ones with haloalkanes

The alkylation of ambident anions of 2-(methylsulfanyl)-6-(polyfluoroalkyl)pyrimidin-4(3H)-ones with 4-bromobutyl acetate leads to concurrent formation of O- and N-(4-acetoxybutyl) derivatives. Polar aprotic solvents favor formation of the O-isomer, and weakly polar dioxane favors N-alkylation. The reaction of 2-(methylsulfanyl)-6-(trifluoromethyl)pyrimidin-4(3H)-one with an equimolar amount of 1,2-dibromoethane in polar acetonitrile gives a mixture of N,N-, O,O-, and N,O-bridged bis-pyrimidines, as well as N- and O-[2-(methylsulfanyl)ethyl] derivatives, whereas in the presence of 10 equiv of 1,2-dibromoethane the N,O-isomer is formed as the only product. The reaction in weakly polar tetrahydrofuran yields N,N- and N,O-bispyrimidines.     

Synthesis and structure of bis(1,2-diaminoethane) copper(II) bis(<Emphasis Type="Italic">o</Emphasis>-hydroxybenzoate) monohydrate and <Emphasis Type="Italic">trans</Emphasis>-diaquabis(1,2-diaminoethane)copper(II) bis(<Emphasis Type="Italic">o</Emphasis>-aminobenzoate)

X-ray structural analysis has been performed for two complex compounds: Cu(en)₂(o-HB)₂H₂O (I) (a = 16.873(4) Å, b = 8.713(2) Å, c = 14.803(3) Å, β = 91.15(2)°, V = 2175.8(8) ų, C2/c, Z = 4, R(F) = 0.0263, 1516 reflections with I > 3σ (I)) and [Cu(en)₂(OH₂)₂]²⁺(o-AB^?)₂ (II) (a = 7.488(5) Å, b = 22.122(8) Å, c = 7.856(5) Å, β = 118.77(2)°, V = 1140.7(11) ų, P2₁/n, Z = 2, R(F) = 0.0432, 1684 reflections with I > 3σ(I)) synthesized under identical conditions (en is ethylenediamine, o-HB is o-hydroxybenzoate, and o-AB is o-aminobenzoate). Although the compounds were assumed to have similar structures and the Cu-Lig bond lengths and the cis and trans angles are acceptable for an octahedral structure, the geometric parameters of o-HB suggest that the copper atom has a plane square environment.     

Graphene oxide promoted synthesis of <Emphasis Type="Italic">p</Emphasis>-phenylenediamine antioxidants

Three p-phenylenediamine antioxidants (p-phenylenediamine-N,N,N′,N′-tetrapropionic acid tetramethyl ester, p-phenylenediamine-N,N,N′-tripropionic acid trimethyl ester, and p-phenylenediamine-N, N′-dipropionic acid dimethyl ester) were successfully synthesized via atom-economic aza-Michael addition of pphenylenediamine to methyl acrylate p-romoted by graphene oxide in water. The synthesized compounds were characterized by NMR, ESI-MS spectra, and elemental analyses. The effects of the solvent and graphene oxide on the reaction were investigated.     

Mitigating Complexity: Cohesion Parameters and Related Topics. I: The Hildebrand Solubility Parameter

The objective of this review in two parts is to present a compact overview of the development of the solubility parameter \(\left( {\delta_{i} } \right)\) concept: from the seminal work of van Laar in 1910, to the contributions of Scatchard, Hildebrand, Scott and Prausnitz, leading finally to the generalized multi-component (multi-dimensional) cohesion parameters, with the Hansen solubility parameter being the most prominent representative. In this first part, physico-chemical aspects concerning \(\delta_{i}\)-related models in solution chemistry and chemical engineering will be presented, and recent theoretical efforts in this field, that is, equation-of-state approaches and computer simulation methods for the estimation of solubility parameters, will be indicated. Indeed, prediction of thermodynamic properties of liquid nonelectrolyte solutions from properties of the corresponding pure constituents has come a long way since the classic studies by Hildebrand and by Scatchard leading to regular solution theory (RST), in which the solubility parameter is the property of central importance. Selected aspects of RST will be discussed, including the influence of T and of P on \(\delta_{i}\) and their reliable estimation, thereby clearing up misconceptions and pointing out pitfalls not generally recognized. Extending the dicussion to supercritical conditions, the use of solubility parameters in supercritical fluid (SCF) technologies will be indicated, focusing on practical implications of some of the unique phenomena happening in the near supercritical region, which provide the basis of SCF extraction in industries devoted to food-processing, nutraceuticals, pharmaceuticals and biotechnology.     

Random packing of monoatomic structures

The dependence of the first coordination number k _n on the packing factor k _y is obtained for four cubic structures: fcc, bcc, simple cubic, and diamond. The k _n (k _y ) dependence is described by a third-degree polynomial k _n = ?71.76782 + 467.78914 k _y ? 925.48451 k _y ² + 603.01146 k _y ³ with the confidence factor R _d = 1. The k _n (k _y ) function has an N loop with a maximum at k _n = 6.32; k _y = 0.454 and a minimum at k _n = 5.84; k _y = 0.573. The tangents intersect the k _n (k _y ) curve at extrema at k _y = 0.4 and k _y = 0.625. Around the N loop, i.e., at 5.84 ≤ k _n ≤ 6.32 and 0.4 ≤ k _y ≤ 0.625, two or three packing factors correspond to a certain value of the coordination number. Therefore, this range of the k _n and k _y values can be defined as a “random packing” region. Estimations presented here agree well with the results of calculations, both geometric and numerical. For monoatomic solids with the random packing parameters, the difference between the specific volumes of the solid and liquid phases is insignificant. The dilatancy effect is possible in the region where ?k _n / ?k _y ≤ 0.     

Ro-vibrating energy states of a diatomic molecule in an empirical potential

An approximate analytical solution of the Schrödinger equation is obtained to represent the rotational–vibrational (ro-vibrating) motion of a diatomic molecule. The ro-vibrating energy states arise from a systematical solution of the Schrödinger equation for an empirical potential (EP) V _±(r) = D _e {1 ? (?/δ)[coth (ηr)]^±1/1 ? (?/δ)}² are determined by means of a mathematical method so-called the Nikiforov–Uvarov (NU). The effect of the potential parameters on the ro-vibrating energy states is discussed in several values of the vibrational and rotational quantum numbers. Moreover, the validity of the method is tested with previous models called the semiclassical (SC) procedure and the quantum mechanical (QM) method. The obtained results are applied to the molecules H₂ and Ar₂.