Crystal Structures of a Bioactive 6′‐Hydroxy Variant of Sisomicin Bound to the Bacterial and Protozoal Ribosomal Decoding Sites

Parasitic infections recognized as neglected tropical diseases are a source of concern for several regions of the world. Aminoglycosides are potent antimicrobial agents that have been extensively studied by biochemical and structural studies in prokaryotes. However, the molecular mechanism of their potential antiprotozoal activity is less well understood. In the present study, we have examined the in vitro inhibitory activities of some aminoglycosides with a 6′‐hydroxy group on ring I and highlight that one of them, 6′‐hydroxysisomicin, exhibits promising activity against a broad range of protozoan parasites. Furthermore, we have conducted X‐ray analyses of 6′‐hydroxysisomicin bound to the target ribosomal RNA A‐sites in order to understand the mechanisms of both its antibacterial and antiprotozoal activities at the molecular level. The unsaturated ring I of 6′‐hydroxysisomicin can directly stack on G1491, which is highly conserved in bacterial and protozoal species, through π–π interaction and fits closer to the guanidine base than the typically saturated and hydroxylated ring I of other structurally related aminoglycosides. Consequently, the compound adopts a lower energy conformation within the bacterial and protozoal A‐sites and makes pseudo pairs to either A or G at position 1408. The A‐site‐selective binding mode strongly suggests that 6′‐hydroxysisomicin is a potential lead for the design of next‐generation aminoglycosides targeting a wide variety of infectious diseases.     

Crystal structure of the bacterial ribosomal decoding site complexed with a synthetic doubly functionalized paromomycin derivative: a new specific binding mode to an a-minor motif enhances in vitro antibacterial activity

The crystal structure of the complex between oligonucleotide containing the bacterial ribosomal decoding site (A site) and the synthetic paromomycin analogue 1, which contains the gamma-amino-alpha-hydroxybutyryl (L-haba) group at position N1 of ring II (2-DOS ring), and an ether chain with an O-phenethylaminoethyl group at position C2' of ring III, is reported. Interestingly, next to the paromomycin analogue 1 specifically bound to the A site, a second molecule of 1 with a different conformation is observed at the crystal packing interface which mimics the A-minor interaction between two bulged-out adenines from the A site and the codon-anticodon stem of the mRNA-tRNA complex. Improved antibacterial activity supports the conclusion that analogue 1 might affect protein synthesis on the ribosome in two different ways: 1) specific binding to the A site forces maintenance of the "on" state with two bulged out adenines, and 2) a new binding mode of 1 to an A-minor motif which stabilizes complex formation between the ribosome and the mRNA-tRNA complex regardless of whether the codon-anticodon stem is of the cognate or near-cognate type.     

Designed spiro-bicyclic analogues targeting the ribosomal decoding center

The bacterial ribosome represents the confirmed biological target for many known antibiotics that interfere with bacterial protein synthesis. Aminoglycosides represent a lead paradigm in RNA molecular recognition and constitute ideal starting points for the design and synthesis of novel RNA binders. Previous rational design approaches of RNA-targeting small molecules have been mainly concentrated on direct functionalization of aminoglycosidic substructures. Herein, we successfully designed and synthesized rigid spirocyclic scaffolds locked in a predicted ribosome-bound "bioactive" conformation. These analogues are able to mimic many of the interactions of the natural products for the A-site, as proven by their obtained binding affinities. The development of an optimized approach for their synthesis and their potential to inhibit protein production in vitro are presented. Our results could be further utilized for the development of analogues with improved antibiotic profiles.     

Organomodified montmorillonite as filler in natural and synthetic rubber

The filler action of dodecylamine (12C) intercalated montmorillonite (MNT) referred to as organomodified montmorillonite (12C‐MNT) up to 4 wt % on natural rubber (NR) and styrene butadiene rubber (SBR) was studied and findings were compared with respect to the unmodified Na‐MNT. X‐ray analysis was used to calculate the interchain separation (R and R′), degree of crystallinity (X_c), and distortion factor (k). It is noted that R and R′ showed the opposite trend, whereas X_c as well as k showed overall increasing trend with an increasing amount of 12C‐MNT on both NR and SBR. For Na‐MNT (1 wt %) filled NR and SBR, the corresponding magnitude of R and R ′ and X_c showed nearly no change, whereas k_c increased significantly. The crosslinking density (v_c) does not show any significant changes in NR, whereas for SBR, it increases with increasing 12C‐MNT as filler. Interestingly, in the case of 1 wt % pure Na‐MNT used as filler for both NR and SBR, v_c was lower compared to the virgin rubbers. Both swelling index (s_i) and sol fraction (Q) do not show any significant variation for NR composites, whereas these decrease for SBR composites with increasing concentration of 12C‐MNT filler. On the contrary, NR and SBR with 1 wt % of Na‐MNT filler show greater magnitude of s_i and Q corresponding to the pure ones. Measurements of mechanical properties showed a significant increase in tensile strength and elongation at break for NR‐12C‐MNT (4 wt %) when compared with either virgin NR. In addition, modulus at the elongation at 100 and 200% in general increases with increasing loading of 12C‐MNT filler in NR. Similar observations were also noted in the case of SBR. Interestingly, when only pure Na‐MNT is used as filler, the strength of NR and SBR decreases drastically. Scanning electron microscopic studies were also to used support the mechanical behavior of NR‐12MNT and SBR‐12CMNT composites. © 2004 Wiley Periodicals, Inc. J Appl Polym Sci 92: 3583–3592, 2004     

Effect of Cu(II) on the complex between kanamycin A and the bacterial ribosomal A site

The solution structure of kanamycin A interacting with a ribosomal A-site fragment was solved by transferred-NOE techniques and found to agree with the structure of the complex observed in the crystal. Despite the fast exchange conditions found for the interaction, the bound form was identified by NOESY spectroscopy. At 600 MHz, NOE effects are only observed for the RNA-associated antibiotic. Dissociation constants were measured by NMR spectroscopy for two sites of interaction (K(d1)=150+/-40 microM; K(d2)=360+/-50 microM). Furthermore, the effects of the Cu(II) ion on the antibiotic, on the RNA fragment that mimics the bacterial ribosomal A site, and on the complex formed between these two entities were analyzed. The study led to the proposal of a model that localizes the copper ion within the kanamycin-RNA complex.     

Binding mode of TMC-95A analogues to eukaryotic 20S proteasome

The complex thermodynamics that govern noncovalent protein-ligand interactions are still not fully understood, despite the exponential increase in experimental structural data available from X-ray crystallography and NMR spectroscopy. The eukaryotic 20S proteasome offers an ideal system for such studies as it contains in duplicate three proteolytically active sites with different substrate specificities. The natural product TMC-95A inhibits these proteolytic centers noncovalently with distinct affinities. X-ray crystallographic analysis of the complexes of the yeast proteasome core particle with this natural inhibitor and two synthetic analogues clearly revealed highly homologous hydrogen-bonding networks involving mainly the peptide backbone despite the strongly differentiated binding affinities to the three active sites of the 20S proteasome. The natural product and the two analogues are constrained in a rigid beta-type extended conformation by the endocyclic biaryl clamp, which preorganizes the peptide backbone for optimal adaptation of the ligands to the active site clefts and thus favors the binding processes entropically. However, the biaryl clamp also dictates the orientation of the P1 and P3 residues and their mode of interaction with the protein binding subsites. This limitation is optimally solved in TMC-95A with the conformationally restricted (Z)-prop-1-enyl group acting as P1 residue, at least for the chymotrypsin-like active site; however, it critically affects the inhibitory potencies of the analogues, thus suggesting the use of less-rigid endocyclic clamps in the design of proteasome inhibitors that allow for a better presentation of residues interacting with the active site clefts of the enzyme.     

Improved gas selectivity of polyetherimide membrane by the incorporation of PIM polyimide phase

The aim of this work was to prepare blend membranes of a polyetherimide (PEI) and different ratios of a microporous polyimide (PIM‐B) in order to obtain an improved material for gas selectivity. Miscibility of the membranes was studied through fourier transform infrared spectroscopy (FTIR), Fluorescence, ultraviolet‐visible spectroscopy (UV–vis), polarize light microscope images, X‐ray diffraction (XRD), and differential scanning calorimetry analysis. Gas permeability assays were also performed. Results showed blends were partially miscible along the different ratios due to the existence of: (i) absorption shoulders at lower wavenumbers on the carbonyl stretching band; (ii) red‐shifting of Fluorescence and UV–vis absorption bands; (iii) decreasing of d‐spacing as the amount of PIM‐B phase increased; and (iv) composition‐dependent glass transition temperatures (T_gs). The mobility selectivity (D_i/j) dominated H₂ and O₂ gas separations. High solubility coefficients (S) linked to PIM‐B microporosity improved the ideal gas selectivity of the blend membranes. PEI/PIM‐B membrane at the ratio of 80/20 showed impressive H₂/CO₂ (8.66) and O₂/N₂ (10.90) gas separation factors. © 2016 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2017 , 134, 44682.     

Elaboration and thermal analysis of nanocomposites based on poly(methyl methacrylate‐co‐4‐vinylpyridine) and Maghnia bentonite

Nanocomposites based on an organically modified bentonite, from Maghnia Algeria (OBT) and a copolymer of methyl methacrylate with 4‐vinylpyridine (PMM4VP) synthesized in dioxan at room temperature using a neutral Ni(II)α‐benzoinoxime complex as a single component initiator, were elaborated via solution intercalation method and characterized by several techniques. X‐ray diffraction and transmission electron microscopy investigations indicate that mainly exfoliated and intercalated PMM4VP/OBT nanocomposites were elaborated and that the degree of exfoliation decreases with an increase of the OBT loading. Thermal analyses of these nanocomposites compared with their virgin copolymer confirmed a significant improvement of their thermal stability as evidenced by an increase of 28°C in their onset degradation temperatures. In addition, differential scanning calorimetry displayed an increase in the range of 12–18°C in their glass transition temperatures relative to their virgin copolymer. © 2013 Wiley Periodicals, Inc. J. Appl. Polym. Sci., 2013     

The fate of iron during the alkali‐activation of synthetic (CaO‐)FeOx‐SiO2 slags: An Fe K‐edge XANES study

Slags from the nonferrous metals industry have great potential to be used as feedstocks for the production of alkali‐activated materials. Until now, however, only very limited information has been available about the structural characteristics of these materials. In the work presented herein, synthetic slags in the CaO–FeO_x–SiO₂ system, representing typical compositions of Fe‐rich slags, and inorganic polymers (IPs) produced from the synthetic slags by activation with alkali silicate solutions have been studied by means of X‐ray absorption near‐edge structure (XANES) spectroscopy at the Fe K‐edge. The iron in the slags was largely Fe²⁺, with an average coordination number of approximately 5 for the iron in the amorphous fraction. The increase in average oxidation number after alkali‐activation was conceptualized as the consequence of slag dissolution and IP precipitation, and employed to calculate the degrees of reaction of the slags. The degree of reaction of the slags increased with increasing amorphous fraction. The iron in the IPs had an average coordination number of approximately 5; thus, IPs produced from the Fe‐rich slags studied here are not Fe‐analogs of aluminosilicate geopolymers, but differ significantly in terms of structure from the latter.     

Synthesis and characterization of calcium‐containing poly(urethane‐urea)s

A calcium salt of mono(hydroxyethoxyethyl)phthalate [Ca(HEEP)2] was synthesized by the reaction of diethylene glycol, phthalic anhydride, and calcium acetate. Four different bisureas like hexamethylene bis(ω,N‐hydroxyethylurea), tolylene 2,4‐bis(ω,N‐hydroxyethylurea), hexamethylene bis(ω,N‐hydroxypropylurea), and tolylene 2,4‐bis(ω,N‐hydroxypropylurea) were prepared by reacting ethanolamine or propanolamine with hexamethylene diisocyanate (HMDI) or tolylene 2,4‐diisocyanate (TDI). Calcium‐containing poly(urethane‐urea)s (PUUs) were synthesized by reacting HMDI or TDI with 1:1 mixtures of Ca(HEEP)2 and each of the bisureas using di‐n‐butyltin dilaurate as a catalyst. The PUUs were well characterized by Fourier transform infrared, 1H‐ and 13C‐NMR (nuclear magnetic resonance), solid‐state 13C cross‐polarization–magic angle spinning NMR, viscosity, solubility, elemental, and X‐ray diffraction studies. Thermal properties of the polymers were also studied by using thermogravimetric analysis and differential scanning calorimetry. © 2003 Wiley Periodicals, Inc. J Appl Polym Sci 90: 3488–3496, 2003     

Enhancement of thermal stability associated with the chemical treatment of bacterial (Gluconacetobacter xylinus) cellulose

Bacterial cellulose produced by Gluconacetobacter xylinus was treated with sodium carbonate (Na₂CO₃) and sodium hydroxide (NaOH) to remove entrapped noncellulosic materials. Fourier transform infrared (FTIR) spectroscopy has been used to investigate the effect of alkali on the chemical structure of bacterial cellulose. The changes in the crystalline nature of these membranes were analyzed using X‐ray diffraction (XRD) technique. The morphology and the removal of noncellulosic impurities followed by alkali treatment were studied using scanning electron microscopy (SEM) and energy dispersive X‐ray spectrometry (EDS). The enhanced thermal stability of bacterial cellulose was evident from thermogravimetric analysis (TGA). Further, the alkali treatments resulted in relatively pure form of cellulose, which finds application in various spheres. © 2008 Wiley Periodicals, Inc. J Appl Polym Sci, 2008     

Phenolic resin‐crosslinked natural rubber/clay nanocomposites: Influence of clay loading and interfacial adhesion on strain‐induced crystallization behavior

Nanocomposites of natural rubber (NR) and pristine clay (clay) were prepared by latex mixing, then crosslinked with phenolic resin (PhOH). For comparative study, the PhOH‐crosslinked neat NR was also prepared. Influence of clay loading (i.e., 1, 3, 5, and 10 phr) on mechanical properties and structural change of PhOH‐crosslinked NR/clay nanocomposites was studied through X‐ray diffraction (XRD), transmission electron microscopic (TEM), wide‐angle X‐ray diffraction (WAXD), tensile property measurement, and Fourier transform infrared spectroscopy (FTIR). XRD and TEM showed that the clay was partly intercalated and aggregated, and that the dispersion state of clay was non‐uniform at higher clay loading (>5 phr). From tensile test measurement, it was found that the pronounced upturn of tensile stress was observed when the clay loading was increased and a maximum tensile strength of the PhOH‐crosslinked NR/clay nanocomposites was obtained at 5 phr clay. WAXD observations showed that an increased addition of clay induced more orientation and alignment of NR chains, thereby lowering onset strain of strain‐induced crystallization and promoting crystallinity of the NR matrix during tensile deformation. FTIR investigation indicated a strong interfacial adhesion between NR matrix and clay filler through a phenolic resin bridge. This suggested that the PhOH did not only act as curative agent for crosslinking of NR, but it also worked as coupling agent for promoting interfacial reaction between NR and clay. The presence of strong interfacial adhesion was found to play an important role in the crystallization process, leading to promotion of mechanical properties of the PhOH‐crosslinked NR/clay nanocomposites. © 2015 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2016 , 133, 43214.     

Adhesion properties of phosphate‐ and siloxane‐containing polyurethane dispersions to steel: An analysis of the metal–coating interface

Polyurethane dispersions containing phosphate and siloxane groups in the main chain were investigated as possible self‐assembling metal coatings. Improved adhesion of the polymer to the metal was observed because of the formation of an insoluble metal phosphate layer at the metal–coating interface. The neutralizing amine of the dispersions affected the formation of this metal phosphate, and the metal phosphate formation was dependent on the curing temperature and boiling point of the amine used for neutralization. A crosscut comparative study of adhesion proved that the phosphate‐containing coatings had better adhesion because of the formation of ionic bonds at the metal–coating interface. A solid‐state adhesion prediction method based on thermodynamic considerations was used. The results of the solid‐state adhesion method correlated well with that obtained from the crosscut adhesion test method. © 2003 Wiley Periodicals, Inc. J Appl Polym Sci 88: 900–907, 2003     

X‐ray absorption spectroscopy study of synthetic cobalt blue pigments similar to Kangxi blue and white porcelain

A series of cobalt blue pigments, which were synthesized based on the chemical compositions of the blue pigments in Kangxi blue and white porcelain, were investigated by Co, Mn, and Fe K‐edge and L_2,3‐edge X‐ray absorption spectroscopy to determine the oxidation states and species of the elements and to discern their impact on the blue color. The results reveal that Co is bivalent and mainly located at tetrahedral sites, which is the main parameter controlling the blue color. Mn is mainly present as Mn²⁺, or Co_xZn_1‐xAl₂O₄ and Fe is mainly present as Fe³⁺. In particular, Fe³⁺ substitutes the Al in CoAl₂O₄ and occupies octahedral sites with a high Mn content. All the synthetic cobalt blue pigments can form a solid solution with various end‐members or an intermediate solution spinel. The spectroscopic determination of the oxidation states and speciation of Co, Mn, and Fe furthers understanding of the coloration of blue pigments in blue and white porcelain.     

Self‐assembling metal coatings from phosphated and siloxane‐modified polyurethane dispersions: An analysis of the coating–air interface

Polyurethane dispersion coatings containing phosphate and siloxane chains were evaluated for their self‐assembling properties for a single‐coating system. Dynamic contact angles (DCAs) and X‐ray photoelectron spectroscopy (XPS) were used to study the coating–air interface. The siloxane chains were the predominant species on the surfaces of the coatings. The wetting properties of the coating–air interface were reversed when the coated panels were immersed in an ionic solution, and the decrease in hydrophobicity was linear with time. Results from XPS and DCA analyses were similar. The self‐assembling properties of the coatings could be useful in the development of hydrophobic coatings from hydrophilic polymers. © 2003 Wiley Periodicals, Inc. J Appl Polym Sci 88: 893–899, 2003     

X‐ray photoelectron spectroscopy and electrical conductivity of polyaniline doped with dodecylbenzenesulfonic acid as a function of the synthetic method

X‐ray photoelectron spectroscopy (XPS) has been employed to investigate the protonation degree of polyaniline doped with dodecylbenzenesulfonic acid (Pani. DBSA) obtained by different synthetic methods. The protonation degree has been compared to electrical conductivity. Pani.DBSA prepared through the redoping process in an agate mortar displays conductivity values within the range of 1 S/cm. A protonation level of 48% with almost all imine groups being protonated. Pani.DBSA was also synthesized by oxidative polymerization of aniline in the presence of DBSA, which acts simultaneously as a surfactant and as protonating agent. This in situ doping polymerization was carried out in aqueous or toluene media. In both cases, protonation degrees higher than 50% have been achieved, indicating that a substantial portion of amine units have also been protonated. Higher doping degree has been achieved by aqueous dispersion polymerization of aniline. The C/N and S/N molar ratios obtained by XPS analysis indicate that the polyaniline chains obtained by in situ polymerization are protonated by both sulfonate and hydrogen sulfate anions. © 2001 John Wiley & Sons, Inc. J Appl Polym Sci 80: 556–565, 2001