Direct in situ measurement of polymorphic transition temperatures under thermo-mechanochemical conditions.

For the first time, we directly measured the onset and completion temperatures of polymorphic transitions under thermo-mechanochemical conditions by simultaneous in situ synchrotron powder X-ray diffraction and temperature monitoring. We determined the thermo-mechanochemical polymorphic transition temperature in 1-adamantyl-1-diamantyl ether to be 31 °C lower than the transition temperature determined by DSC. Our findings highlight the uniqueness of thermo-mechanochemical conditions, with potential applications in polymorph screening.

New resveratrol analogs as improved biologically active structures: Design, synthesis and computational modeling.

New analogs of the well-known bioactive trihydroxy-stilbene resveratrol were synthesized to investigate their potential biological activity. The focus was on assessing their ability to inhibit cholinesterase enzymes (ChEs) and their antioxidative properties, which were thoroughly examined. New resveratrol analogs were synthesized through Wittig or McMurry reaction in moderate-to-good yields. In all synthetic pathways, mixtures of cis- and trans-isomers were obtained, then separated by chromatography, and trans-isomers were isolated as targeted structures. The stilbene derivatives underwent evaluation for antioxidant activity (AOA) using DPPH and CUPRAC assay, and their potential to inhibit acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) was also measured. The biological tests have shown that the same compounds exhibited significant antioxidative and butyrylcholinesterase inhibitory potential, as evidenced by lower IC50 values compared to the established standards, trans-resveratrol, and galantamine, respectively. Additionally, molecular docking of the selected synthesized potential inhibitors to the enzyme's active site was performed, followed by assessing the complex stability using molecular dynamics simulation lasting 100 ns. Lastly, the new compounds underwent examination to determine their potential mutagenicity.

Interfacial Water Molecules as Agents for Phase Change Control and Proton Conductivity Enhancement in the Ammonium Vanadyl Tartrate System.

This study demonstrates the reversible structural transformation, single-crystal-to-single-crystal, of the ammonium vanadyl (L-tartrate) complex salt from the hydrate phase to the anhydrous phase. The transformation can be initiated by stimuli, such as temperature, humidity, or vacuum conditions. The hydrate and anhydrous phases exhibit a tetragonal structure (P41212), with marked differences in hydrogen bonding due to the presence or absence of one water molecule per asymmetric unit. The intricate relationship between crystal packing and intermolecular interactions in the hydrate phase was investigated by crystallographic charge density analysis revealing, at the molecular level, the reasons for the observed 5 orders of magnitude higher proton conductivity of the hydrate phase compared to that of the anhydrous phase. To gain further insight into the processes occurring at the surfaces of grain boundaries and the proton transfer mechanisms in this system, rehydration of the complex salt was carried out by using D2O instead of H2O and monitored by in situ ATR-FTIR spectroscopy. The results highlight the critical role of interfacial water molecules in driving structural transformations and influencing proton conductivity.

(N-Alkyloxalamido)-Amino Acid Amides as the Superior Thixotropic Phase Selective Gelators of Petrol and Diesel Fuels.

(N-Alkyloxalamido)-amino acid amides 9-12 exhibit excellent gelation capacities toward some lipophilic solvents as well as toward the commercial fuels, petrol and diesel. Gelator 10 exhibits an excellent phase-selective gelation (PSG) ability and also possesses the highest gelation capacity toward petrol and diesel known to date, with minimum gelation concentration (MGC) values (%, w/v) as low as 0.012 and 0.015, respectively. The self-assembly motif of 10 in petrol and toluene gel fibres is determined from xerogel X-ray powder diffraction (XRPD) data via the simulated annealing procedure (SA) implemented in the EXPO2014 program and refined using the Rietveld method. The elucidated motif is strongly supported by the NMR (NOE and variable temperature) study of 10 toluene-d8 gel. It is shown that the triple unidirectional hydrogen bonding between gelator molecules involving oxalamide and carboxamide groups, together with their very low solubility, results in the formation of gel fibres of a very high aspect ratio (d = 10-30 nm, l = 0.6-1.3 µm), resulting in the as-yet unprecedented capacity of gelling commercial fuels. Rheological measurements performed at low concentrations of 10 confirmed the strength of the self-assembled network with the desired thixotropic properties that are advantageous for multiple applications. Instantaneous phase-selective gelation was obtained at room temperature through the addition of the 10 solution to the biphasic mixture of diesel and water in which the carrier solvent was congealed along with the diesel phase. The superior gelling properties and PSG ability of 10 may be used for the development of more efficient marine and surface oil spill recovery and waste water treatment technologies as well as the development of safer fuel storage and transport technologies.

The pursuit of new alternative ways to eradicate Helicobacter pylori continues: Detailed characterization of interactions in the adenylosuccinate synthetase active site.

Purine nucleotide synthesis is realised only through the salvage pathway in pathogenic bacterium Helicobacter pylori. Therefore, the enzymes of this pathway, among them also the adenylosuccinate synthetase (AdSS), present potential new drug targets. This paper describes characterization of His6-tagged AdSS from H. pylori. Thorough analysis of 3D-structures of fully ligated AdSS (in a complex with guanosine diphosphate, 6-phosphoryl-inosine monophosphate, hadacidin and Mg2+) and AdSS in a complex with inosine monophosphate (IMP) only, enabled identification of active site interactions crucial for ligand binding and enzyme activity. Combination of experimental and molecular dynamics (MD) simulations data, particularly emphasized the importance of hydrogen bond Arg135-IMP for enzyme dimerization and active site formation. The synergistic effect of substrates (IMP and guanosine triphosphate) binding was suggested by MD simulations. Several flexible elements of the structure (loops) are stabilized by the presence of IMP alone, however loops comprising residues 287-293 and 40-44 occupy different positions in two solved H. pylori AdSS structures. MD simulations discovered the hydrogen bond network that stabilizes the closed conformation of the residues 40-50 loop, only in the presence of IMP. Presented findings provide a solid basis for the design of new AdSS inhibitors as potential drugs against H. pylori.

Preparation and characterization of non-aromatic ether self-assemblies on a HOPG surface.

On-surface self-assemblies of aromatic organic molecules have been widely investigated, but the characterization of analogous self-assemblies consisting of fully sp3-hybridized molecules remains challenging. The possible on-surface orientations of alkyl molecules not exclusively comprised of long alkyl chains are difficult to distinguish because of their inherently low symmetry and non-planar nature. Here, we present a detailed study of diamondoid ethers, structurally rigid and fully saturated molecules, which form uniform 2D monolayers on a highly oriented pyrolytic graphite (HOPG) surface. Using scanning tunneling microscopy, various computational tools, and x-ray structural analysis, we identified the most favorable on-surface orientations of these rigid ethers and accounted for the forces driving the self-organization process. The influence of the oxygen atom and London dispersion interactions were found to be responsible for the formation of the observed highly ordered 2D ether assemblies. Our findings provide insight into the on-surface properties and behavior of non-aromatic organic compounds and broaden our understanding of the phenomena characteristic of monolayers consisting of non-planar molecules.

Synthesis of 14-membered enediyne-embedded macrocycles.

A concise and practical strategy towards a novel class of 14-membered macrocycles containing an enediyne (Z-3-ene-1,5-diyne) structural unit is described. A highly modular assembly of various precursors via sequential Ugi/Sonogashira reactions allowed the preparation of hybrid enediyne-peptide macrocycles in most cases as single diastereoisomers. Selected macrocyclic compounds showed moderate antiproliferative activity, and can be considered as templates suitable for further diversification in terms of ring size, shape, and stereochemistry.

Interactions of 2,6-substituted purines with purine nucleoside phosphorylase from Helicobacter pylori in solution and in the crystal, and the effects of these compounds on cell cultures of this bacterium.

Helicobacter pylori represents a global health threat with around 50% of the world population infected. Due to the increasing number of antibiotic-resistant strains, new strategies for eradication of H. pylori are needed. In this study, we suggest purine nucleoside phosphorylase (PNP) as a possible new drug target, by characterising its interactions with 2- and/or 6-substituted purines as well as the effect of these compounds on bacterial growth. Inhibition constants are in the micromolar range, the lowest being that of 6-benzylthio-2-chloropurine. This compound also inhibits H. pylori 26695 growth at the lowest concentration. X-ray structures of the complexes of PNP with the investigated compounds allowed the identification of interactions of inhibitors in the enzyme's base-binding site and the suggestion of structures that could bind to the enzyme more tightly. Our findings prove the potential of PNP inhibitors in the design of drugs against H. pylori.

Gamma Radiation- and Ultraviolet-Induced Polymerization of Bis(amino acid)fumaramide Gel Assemblies.

Controlling the polymerization of supramolecular self-assembly through external stimuli holds great potential for the development of responsive soft materials and manipulation at the nanoscale. Vinyl esters of bis(leu or val)fumaramide (1a and 2a) have been found to be gelators of various organic solvents and were applied in this investigation of the influence of organogelators' self-assembly on solid-state polymerization induced by gamma and ultraviolet irradiation. Here, we report our investigation into the influences of self-assemblies of bis(amino acid vinyl ester)fumaramides on gamma-ray- and ultraviolet-induced polymerization. The gelator molecules self-assembled by non-covalent interactions, mainly through hydrogen bonds between the amide group (CONH) and the carboxyl group (COO), thus forming a gel network. NMR and FTIR spectroscopy were used to investigate and characterize supramolecular gels. TEM and SEM microscopy were used to investigate the morphology of gels and polymers. Morphology studies showed that the gels contained a filamentous structure of nanometer dimensions that was exhaustive in a three-dimensional network. The prepared derivatives contained reactive alkyl groups suitable for carrying out the polymerization reaction initiated by gamma or ultraviolet radiation in the supramolecular aggregates of selected gels. It was found that the polymerization reaction occurred only in the network of the gel and was dependent on the structure of aggregates or the proximity and orientation of double bonds in the gel network. Polymers were formed by the gels exposure to gamma and ultraviolet radiation in toluene, and water/DMF gels with transcripts of their gel structure into polymers. The polymeric material was able to immobilize various solvents by swelling. Furthermore, methyl esters of bis(leu and val)fumaramide (1b and 2b) were synthesized; these compounds showed no gelling properties, and the crystal structure of the valine derivative 2b was determined.

N-Alkylated C-Glycosyl Amino Acid Derivatives: Synthesis by a One-Pot Four-Component Ugi Reaction.

C-glycosides represent an important group of naturally occurring glycosylation derivatives but are also efficient mimetics of native O-glycosides. Here, a one-pot four-component methodology is described toward a library of N-alkylated C-glycosyl amino acid derivatives comprising seven different isopropylidene-protected carbohydrate units. The applied methodology tolerates different amines and isocyanides and provides access to Ugi products in yields up to 85 %. X-ray analysis of selected products bearing three different carbohydrate motifs and comparison of their crystal structures with similar ones deposited in Cambridge Crystallographic Database revealed that four structures adopt different conformations, mostly not typical for peptide structures. This property opens the possibility to exploit here described N-alkylated C-glycosyl amino acid derivatives as templates to access different biotic and abiotic secondary structures.

Matrix material structure dependence of the embedded electron spin decoherence.

In this article, we present the novel application of the nuclear spin bath model and the cluster correlation expansion method on studying the matrix material structure via embedded electron spin decoherence. Profiles of embedded electron spin decoherence under the Carr-Purcell-Meiboom-Gill dynamical decoupling pulse series in a model system for organic solids (malonic acid) are calculated for different structures. Resulting decay profiles exhibit a strong correlation to the variations of an adjacent proton environment among them. In addition, the decoherence behavior of embedded spin in proton spin bath(s) of organic solids is found to be significantly different from bath models with other nuclei through the violation of the even-odd pulse parity, which characterizes the influence of large dipolar coupling between protons at the quantum level. Theoretical predictions of decoherence profiles in polycrystalline, the relative distribution of Hahn echo signal decay time scales among single crystal orientations, and the reduction in Hahn echo signal decay time scale by disorder are positively verified by experiments.

Crystallographic snapshots of ligand binding to hexameric purine nucleoside phosphorylase and kinetic studies give insight into the mechanism of catalysis.

Purine nucleoside phosphorylase (PNP) catalyses the cleavage of the glycosidic bond of purine nucleosides using phosphate instead of water as a second substrate. PNP from Escherichia coli is a homohexamer, build as a trimer of dimers, and each subunit can be in two conformations, open or closed. This conformational change is induced by the presence of phosphate substrate, and very likely a required step for the catalysis. Closing one active site strongly affects the others, by a yet unclear mechanism and order of events. Kinetic and ligand binding studies show strong negative cooperativity between subunits. Here, for the first time, we managed to monitor the sequence of nucleoside binding to individual subunits in the crystal structures of the wild-type enzyme, showing that first the closed sites, not the open ones, are occupied by the nucleoside. However, two mutations within the active site, Asp204Ala/Arg217Ala, are enough not only to significantly reduce the effectiveness of the enzyme, but also reverse the sequence of the nucleoside binding. In the mutant the open sites, neighbours in a dimer of those in the closed conformation, are occupied as first. This demonstrates how important for the effective catalysis of Escherichia coli PNP is proper subunit cooperation.

Helicobacter pylori purine nucleoside phosphorylase shows new distribution patterns of open and closed active site conformations and unusual biochemical features.

Even with decades of research, purine nucleoside phosphorylases (PNPs) are enzymes whose mechanism is yet to be fully understood. This is especially true in the case of hexameric PNPs, and is probably, in part, due to their complex oligomeric nature and a whole spectrum of active site conformations related to interactions with different ligands. Here we report an extensive structural characterization of the apo forms of hexameric PNP from Helicobacter pylori (HpPNP), as well as its complexes with phosphate (Pi ) and an inhibitor, formycin A (FA), together with kinetic, binding, docking and molecular dynamics studies. X-ray structures show previously unseen distributions of open and closed active sites. Microscale thermophoresis results indicate that a two-site model describes Pi binding, while a three-site model is needed to characterize FA binding, irrespective of Pi presence. The latter may be related to the newly found nonstandard mode of FA binding. The ternary complex of the enzyme with Pi and FA shows, however, that Pi binding stabilizes the standard mode of FA binding. Surprisingly, HpPNP has low affinity towards the natural substrate adenosine. Molecular dynamics simulations show that Pi moves out of most active sites, in accordance with its weak binding. Conformational changes between nonstandard and standard binding modes of nucleoside are observed during the simulations. Altogether, these findings show some unique features of HpPNP and provide new insights into the functioning of the active sites, with implications for understanding the complex mechanism of catalysis of this enzyme. DATABASES: The atomic coordinates and structure factors have been deposited in the Protein Data Bank: with accession codes 6F52 (HpPNPapo_1), 6F5A (HpPNPapo_2), 6F5I (HpPNPapo_3), 5LU0 (HpPNP_PO4), 6F4W (HpPNP_FA) and 6F4X (HpPNP_PO4_FA). ENZYMES: Purine nucleoside orthophosphate ribosyl transferase, EC2.4.2.1, UniProtID: P56463.

Controlling orthogonal self-assembly through cis-trans isomerization of a non-covalent palladium complex dimer.

The trans-configured square-planar complex of dichloropalladium and chiral monodentate phosphine ligands forms self-complementary dimers through 16 hydrogen bonded amides and π-π stacking in chlorinated solvents. The self-assembly is controlled by cis-trans isomerisation of the metal center, where the trans-configuration governs the dimer formation.

Catalytic Dyad in the SGNH Hydrolase Superfamily: In-depth Insight into Structural Parameters Tuning the Catalytic Process of Extracellular Lipase from Streptomyces rimosus.

SrLip is an extracellular enzyme from Streptomyces rimosus (Q93MW7) exhibiting lipase, phospholipase, esterase, thioesterase, and tweenase activities. The structure of SrLip is one of a very few lipases, among the 3D-structures of the SGNH superfamily of hydrolases, structurally characterized by synchrotron diffraction data at 1.75 Å resolution (PDB: 5MAL ). Its crystal structure was determined by molecular replacement using a homology model based on the crystal structure of phospholipase A1 from Streptomyces albidoflavus (PDB: 4HYQ ). The structure reveals the Rossmann-like 3-layer αßα sandwich fold typical of the SGNH superfamily stabilized by three disulfide bonds. The active site shows a catalytic dyad involving Ser10 and His216 with Ser10-OγH···NεHis216, His216-NδH···O═C-Ser214, and Gly54-NH···Oγ-Ser10 hydrogen bonds essential for the catalysis; the carbonyl oxygen of the Ser214 main chain acts as a hydrogen bond acceptor ensuring the orientation of the His216 imidazole ring suitable for a proton transfer. Molecular dynamics simulations of the apoenzyme and its complex with p-nitrophenyl caprylate were used to probe the positioning of the substrate ester group within the active site and its aliphatic chain within the binding site. Quantum-mechanical calculations at the DFT level revealed the precise molecular mechanism of the SrLip catalytic activity, demonstrating that the overall hydrolysis is a two-step process with acylation as the rate-limiting step associated with the activation free energy of ΔG⧧ENZ = 17.9 kcal mol-1, being in reasonable agreement with the experimental value of 14.5 kcal mol-1, thus providing strong support in favor of the proposed catalytic mechanism based on a dyad.

Structural characterization of purine nucleoside phosphorylase from human pathogen Helicobacter pylori.

Microaerophilic bacterium Helicobacer pylori is a well known human pathogen involved in the development of many diseases. Due to the evergrowing infection rate and increase of H. pylori antibiotic resistence, it is of utmost importance to find a new way to attack and eradicate H. pylori. The purine metabolism in H. pylori is solely dependant on the salvage pathway and one of the key enzymes in this pathway is purine nucleoside phosphorylase (PNP). In this timely context, we report here the basic biochemical and structural characterization of recombinant PNP from the H. pylori clinical isolate expressed in Escherichia coli. Structure of H. pylori PNP is typical for high molecular mass PNPs. However, its activity towards adenosine is very low, thus resembling more that of low molecular mass PNPs. Understanding the molecular mechanism of this key enzyme may lead to the development of new drug strategies and help in the eradication of H. pylori.

Interplay of Noncovalent Interactions in Ionic Liquid/Sodium Bis(2-ethylhexyl) Sulfosuccinate Mixtures: From Lamellar to Bicontinuous Cubic Liquid Crystalline Phase.

Phase transitions in mixtures of imidazolium based ionic liquid ([C12mim]Br) and anionic double tail surfactant, sodium bis(2-ethylhexyl) sulfosuccinate (AOT), were studied using a multitechnique approach. The system was primarily chosen for its expected ability to form a variety of lamellar and nonlamellar liquid crystalline phases which can transform into each other via different mechanisms. Depending on the bulk composition and total surfactant concentration, mixed micelles, coacervates, and lamellar and inverse bicontinuous cubic liquid crystalline phase were observed. Along with electrostatic attractions and geometric packing constraints, additional noncovalent interactions (hydrogen bonding, π-π stacking) enhanced attractive interactions and stabilized low curvature aggregates. At stoichiometric conditions, coexistence of coacervates and vesicles was found at lower, while bicontinuous cubic phase and vesicles were present at higher total surfactant concentrations. The phase transitions from a dispersed lamellar to inverse cubic bicontinuous phase occur as a consequence of charge shielding and closer packing of oppositely charged headgroups followed by a change in bilayer curvature. Transition is continuous with both phases coexisting over a relatively broad range of concentrations and very likely involves a sponge-like phase as a structural intermediate. To the best of our knowledge, this type of phase transition has not been observed before in surface active ionic liquid/surfactant mixtures.

Structure-property relationship of quinuclidinium surfactants--Towards multifunctional biologically active molecules.

Motivated by diverse biological and pharmacological activity of quinuclidine and oxime compounds we have synthesized and characterized novel class of surfactants, 3-hydroxyimino quinuclidinium bromides with different alkyl chains lengths (CnQNOH; n=12, 14 and 16). The incorporation of non conventional hydroxyimino quinuclidinium headgroup and variation in alkyl chain length affects hydrophilic-hydrophobic balance of surfactant molecule and thereby physicochemical properties important for its application. Therefore, newly synthesized surfactants were characterized by the combination of different experimental techniques: X-ray analysis, potentiometry, electrical conductivity, surface tension and dynamic light scattering measurements, as well as antimicrobial susceptibility tests. Comprehensive investigation of CnQNOH surfactants enabled insight into structure-property relationship i.e., way in which the arrangement of surfactant molecules in the crystal phase correlates with their solution behavior and biologically activity. The synthesized CnQNOH surfactants exhibited high adsorption efficiency and relatively low critical micelle concentrations. In addition, all investigated compounds showed very potent and promising activity against Gram-positive and clinically relevant Gram-negative bacterial strains compared to conventional antimicrobial agents: tetracycline and gentamicin. The overall results indicate that bicyclic headgroup with oxime moiety, which affects both hydrophilicity and hydrophobicity of CnQNOH molecule in addition to enabling hydrogen bonding, has dominant effect on crystal packing and physicochemical properties. The unique structural features of cationic surfactants with hydroxyimino quinuclidine headgroup along with diverse biological activity have made them promising structures in novel drug discovery. Obtained fundamental understanding how combination of different functionalities in a single surfactant molecule affects its physicochemical properties represents a good starting point for further biological research.

Inhibition of extracellular lipase from Streptomyces rimosus with 3,4-dichloroisocoumarin.

Kinetic characterization of lipase inhibition was performed by activity measurement and mass spectrometry (MS), for the first time with serine-protease inhibitor 3,4-dichloroisocoumarin (DCI). Inhibition of Streptomyces rimosus extracellular lipase (SrLip), a member of the SGNH superfamily, by means of DCI follows the mechanism of two-step irreversible inhibition. The dissociation constant of the noncovalent E•I complex and first-order rate constant for inactivation were determined by incubation (Ki* = 26.6 ± 2.8 µM, k2 = 12.2 ± 0.6 min-1) or progress curve (Ki* = 6.5 ± 1.5 µM, k2 = 0.11 ± 0.01 min-1) method. Half-times of reactivation for lipase inhibited with 10-fold molar excess of DCI were determined by activity measurement (t1/2 = 11.3 ± 0.2 h), matrix-assisted laser desorption/ionization (MALDI, t1/2 = 13.5 ± 0.4 h), and electro-spray ionization (ESI, t1/2 = 12.2 ± 0.5 h) MS. The active SrLip concentration was determined by incubating the enzyme with near equimolar concentrations of DCI, followed by activity and MS measurement.

Intermolecular central to axial chirality transfer in the self-assembled biphenyl containing amino acid-oxalamide gelators.

Chiral amino acid and biphenyl incorporating oxalamide gelators 4-7 with large, 9 bond distance between chiral centres and biphenyl units have been studied. CD investigation of 4-octanol gel and the crystal structure of rac-4 reveal that efficient central to axial chirality transfer occurs by intermolecular interactions in gel and solid state assemblies.