Complex Inhibitory Mechanism of Glycomimetics with Heparanase.

Heparanase (HPSE) is the only mammalian endo-ß-glucuronidase known to catalyze the degradation of heparan sulfate. Dysfunction of HPSE activity has been linked to several disease states, resulting in HPSE becoming the target of numerous therapeutic programs, yet no drug has passed clinical trials to date. Pentosan polysulfate sodium (PPS) is a heterogeneous, FDA-approved drug for the treatment of interstitial cystitis and a known HPSE inhibitor. However, due to its heterogeneity, characterization of its mechanism of HPSE inhibition is challenging. Here, we show that inhibition of HPSE by PPS is complex, involving multiple overlapping binding events, each influenced by factors such as oligosaccharide length and inhibitor-induced changes in the protein secondary structure. The present work advances our molecular understanding of the inhibition of HPSE and will aid in the development of therapeutics for the treatment of a broad range of pathologies associated with enzyme dysfunction, including cancer, inflammatory disease, and viral infections.

A Rapid and Mild Sulfation Strategy Reveals Conformational Preferences in Therapeutically Relevant Sulfated Xylooligosaccharides.

Although sulfated xylooligosaccharides are promising therapeutic leads for a multitude of afflictions, the structural complexity and heterogeneity of commercially deployed forms (e. g. Pentosan polysulfate 1) complicates their path to further clinical development. We describe herein the synthesis of the largest homogeneous persulfated xylooligomers prepared to date, comprising up to eight xylose residues, as standards for biological studies. Near quantitative sulfation was accomplished using a remarkably mild and operationally simple protocol which avoids the need for high temperatures and a large excess of the sulfating reagent. Moreover, the sulfated xylooligomer standards so obtained enabled definitive identification of a pyridinium contaminant in a sample of a commercially prepared Pentosan drug and provided significant insights into the conformational preferences of the constituent persulfated monosaccharide residues. As the spatial distribution of sulfates is a key determinant of the binding of sulfated oligosaccharides to endogenous targets, these findings have broad implications for the advancement of Pentosan-based treatments.

An unexpected vestigial protein complex reveals the evolutionary origins of an s-triazine catabolic enzyme.

Cyanuric acid is a metabolic intermediate of s-triazines, such as atrazine (a common herbicide) and melamine (used in resins and plastics). Cyanuric acid is mineralized to ammonia and carbon dioxide by the soil bacterium Pseudomonas sp. strain ADP via three hydrolytic enzymes (AtzD, AtzE, and AtzF). Here, we report the purification and biochemical and structural characterization of AtzE. Contrary to previous reports, we found that AtzE is not a biuret amidohydrolase, but instead it catalyzes the hydrolytic deamination of 1-carboxybiuret. X-ray crystal structures of apo AtzE and AtzE bound with the suicide inhibitor phenyl phosphorodiamidate revealed that the AtzE enzyme complex consists of two independent molecules in the asymmetric unit. We also show that AtzE forms an α2ß2 heterotetramer with a previously unidentified 68-amino acid-long protein (AtzG) encoded in the cyanuric acid mineralization operon from Pseudomonas sp. strain ADP. Moreover, we observed that AtzG is essential for the production of soluble, active AtzE and that this obligate interaction is a vestige of their shared evolutionary origin. We propose that AtzEG was likely recruited into the cyanuric acid-mineralizing pathway from an ancestral glutamine transamidosome that required protein-protein interactions to enforce the exclusion of solvent from the transamidation reaction.

Hyperthermophilic Carbamate Kinase Stability and Anabolic In Vitro Activity at Alkaline pH.

Carbamate kinases catalyze the conversion of carbamate to carbamoyl phosphate, which is readily transformed into other compounds. Carbamate forms spontaneously from ammonia and carbon dioxide in aqueous solutions, so the kinases have potential for sequestrative utilization of the latter compounds. Here, we compare seven carbamate kinases from mesophilic, thermophilic, and hyperthermophilic sources. In addition to the known enzymes from Enterococcus faecalis and Pyrococcus furiosus, the previously unreported enzymes from the hyperthermophiles Thermococcus sibiricus and Thermococcus barophilus, the thermophiles Fervidobacterium nodosum and Thermosipho melanesiensis, and the mesophile Clostridium tetani were all expressed recombinantly, each in high yield. Only the clostridial enzyme did not show catalysis. In direct assays of carbamate kinase activity, the three hyperthermophilic enzymes display higher specific activities at elevated temperatures, greater stability, and remarkable substrate turnover at alkaline pH (9.9 to 11.4). Thermococcus barophilus and Thermococcus sibiricus carbamate kinases were found to be the most active when the enzymes were tested at 80°C, and maintained activity over broad temperature and pH ranges. These robust thermococcal enzymes therefore represent ideal candidates for biotechnological applications involving aqueous ammonia solutions, since nonbuffered 0.0001 to 1.0 M solutions have pH values of approximately 9.8 to 11.8. As proof of concept, here we also show that carbamoyl phosphate produced by the Thermococcus barophilus kinase is efficiently converted in situ to carbamoyl aspartate by aspartate transcarbamoylase from the same source organism. Using acetyl phosphate to simultaneously recycle the kinase cofactor ATP, at pH 9.9 carbamoyl aspartate is produced in high yield and directly from solutions of ammonia, carbon dioxide, and aspartate.IMPORTANCE Much of the nitrogen in animal wastes and used in fertilizers is commonly lost as ammonia in water runoff, from which it must be removed to prevent downstream pollution and evolution of nitrogenous greenhouse gases. Since carbamate kinases transform ammonia and carbon dioxide to carbamoyl phosphate via carbamate, and carbamoyl phosphate may be converted into other valuable compounds, the kinases provide a route for useful sequestration of ammonia, as well as of carbon dioxide, another greenhouse gas. At the same time, recycling the ammonia in chemical synthesis reduces the need for its energy-intensive production. However, robust catalysts are required for such biotransformations. Here we show that carbamate kinases from hyperthermophilic archaea display remarkable stability and high catalytic activity across broad ranges of pH and temperature, making them promising candidates for biotechnological applications. We also show that carbamoyl phosphate produced by the kinases may be efficiently used to produce carbamoyl aspartate.

Detection of Biosynthetic Precursors, Discovery of Glycosylated Forms, and Homeostasis of Calcitonin in Human Cancer Cells.

The peptide hormone calcitonin is intimately connected with human cancer development and proliferation. Its biosynthesis is reasoned to proceed via glycine-, α-hydroxyglycine-, glycyllysine-, and glycyllysyllysine-extended precursors; however, as a result of the limitations of current analytical methods, until now, there has been no procedure capable of detecting these individual species in cell or tissue samples. Therefore, their presence and dynamics in cancer had not been established. Here, we report the first methodology for the separation, detection, and quantification of calcitonin and each of its precursors in human cancer cells. We also report the discovery and characterization of O-glycosylated calcitonin and its analogous biosynthetic precursors. Through direct and simultaneous analysis of the glycosylated and nonglycosylated species, we interrogate the hormone biosynthesis. This shows that the cellular calcitonin level is maintained to mitigate effects of biosynthetic enzyme inhibitors that substantially change the proportions of calcitonin-related species released into the culture medium.

Specific binding of a ß-cyclodextrin dimer to the amyloid ß peptide modulates the peptide aggregation process.

Alzheimer's disease involves progressive neuronal loss. Linked to the disease is the amyloid ß (Aß) peptide, a 38-43-amino acid peptide found in extracellular amyloid plaques in the brain. Cyclodextrins are nontoxic, cone-shaped oligosaccharides with a hydrophilic exterior and a hydrophobic cavity making them suitable hosts for aromatic guest molecules in water. ß-Cyclodextrin consists of seven α-d-glucopyranoside units and has been shown to reduce the level of fibrillation and neurotoxicity of Aß. We have studied the interaction between Aß and a ß-cyclodextrin dimer, consisting of two ß-cyclodextrin monomers connected by a flexible linker. The ß-cyclodextrin monomer has been found to interact with Aß(1-40) at sites Y10, F19, and/or F20 with a dissociation constant (K(D)) of 3.9 ± 2.0 mM. Here (1)H-(15)N and (1)H-(13)C heteronuclear single-quantum correlation nuclear magnetic resonance (NMR) spectra show that in addition, the ß-cyclodextrin monomer and dimer bind to the histidines. NMR translational diffusion experiments reveal the increased affinity of the ß-cyclodextrin dimer (apparent K(D) of 1.1 ± 0.5 mM) for Aß(1-40) compared to that of the ß-cyclodextrin monomer. Kinetic aggregation experiments based on thioflavin T fluorescence indicate that the dimer at 0.05-5 mM decreases the lag time of Aß aggregation, while a concentration of 10 mM increases the lag time. The ß-cyclodextrin monomer at a high concentration decreases the lag time of the aggregation. We conclude that cyclodextrin monomers and dimers have specific, modulating effects on the Aß(1-40) aggregation process. Transmission electron microscopy shows that the regular fibrillar aggregates formed by Aß(1-40) alone are replaced by a major fraction of amorphous aggregates in the presence of the ß-cyclodextrin dimer.

Prohormone-substrate peptide sequence recognition by peptidylglycine α-amidating monooxygenase and its reflection in increased glycolate inhibitor potency.

The interactions of nineteen peptide substrates and fifteen analogous peptidomimetic glycolate inhibitors with human peptidylglycine α-amidating monooxygenase (PAM) have been investigated. The substrates and inhibitors are the prohormones of calcitonin and oxytocin and their analogues. PAM both secreted into the medium by and extracted from DMS53 small lung carcinoma cells has been studied. The results show that recognition of the prooxytocin and procalcitonin peptide sequences by the enzyme extends more than four and five amino acid residues, respectively, from their C-termini. This substrate sequence recognition is mirrored by increased inhibitor potency with increased peptide length in the glycolate peptidomimetics. Substitution of the C-terminal penultimate glycine and proline residues of prooxytocin and procalcitonin and their analogues with phenylalanine increases the enzyme binding affinity. However, this changes the binding mode from one that depends on peptide sequence recognition to another primarily determined by the phenylalanine moiety, for both the substrates and analogous glycolate inhibitors.

A Simple Recombinant E. coli Cell Lysate-Based Biocatalyst for ATP-Dependent Multi-step Reactions.

The utility of ATP-dependent multi-enzymatic reactions is limited by their requirement for stoichiometric amounts of this expensive cofactor or additional purified enzymes for its recycling. Here we describe a simple method for the production of recombinant cell-free extracts (or lysates) of E. coli that support ATP-dependent biotransformations. The inexpensive preparation described is obtained with modest processing from a single recombinant bacterial culture of E. coli. In addition to recombinantly overexpressed enzymes that catalyze the primary ATP-dependent reactions of interest, endogenous kinases that are naturally present in the extract catalyze recycling of the requisite ATP. This means that only catalytic amounts of cofactor are necessary to drive the biotransformation, and without the requirement for additional purified enzymes. This approach has been applied successfully to an array of in vitro enzymatic cascades with multiple ATP-dependent steps.

Organometallic flow chemistry: solvento complexes.

Photolysis under optimised flow conditions of metal carbonyls [{Ln}M(CO)x] [{Ln}M(CO)x = Cr(CO)6, Mo(CO)6, W(CO)6, Mn(CO)3(η-C5H4Me), Re(CO)3(η-C5H5)] in tetrahydrofuran (THF) conveniently affords the synthetically versatile and labile solvento complexes [{Ln}M(CO)x-1(THF)], thereby obviating many of the caveats associated with photochemical syntheses using either 'batch' or falling film techniques. Conversions were optimised and yields assayed by a combination of in situ infrared spectroscopy and derivatisation as the corresponding triphenylphosphine complexes [{Ln}M(CO)x-1(PPh3)].

Biocompatible Macrocyclization between Cysteine and 2-Cyanopyridine Generates Stable Peptide Inhibitors.

Peptides featuring an N-terminal cysteine residue and the unnatural amino acid 3-(2-cyano-4-pyridyl)alanine (Cpa) cyclize spontaneously in aqueous solution at neutral pH. Cpa is readily available and easily introduced into peptides using standard solid-phase peptide synthesis. The reaction is orthogonal to all proteinogenic amino acids, including cysteine residues that are not at the N-terminus. A substrate peptide of the Zika virus NS2B-NS3 protease cyclized in this way produced an inhibitor of high affinity and proteolytic stability.

Molecular fibers and wires in solid-state and solution self-assemblies of cyclodextrin [2]rotaxanes.

Cyclodextrin [2]rotaxanes have been prepared by coupling dimethylanilines with dicarboxylic acids using DMT-MM, in aqueous solutions of alpha-cyclodextrin, and the example illustrated shows unusual fluorescence emission and other spectroscopic behavior characteristic of the formation of molecular wires in solution, similar to the fibers observed in the solid state.

Fluorescence resonance energy transfer across a mechanical bond of a rotaxane.

Fluorescence transfer across a donor-acceptor tagged rotaxane was studied and a small conformational change of the rotaxane observed using fluorescent spectroscopy and ROESY NMR.

A Cyclodextrin-Based Photoresponsive Molecular Gate that Functions Independently of Either Solvent or Potentially Competitive Guests.

The photoinduced interconversion between cinnamido-substituted cyclodextrins constitutes a gating switch through which the substituent moves to open or block access to the cyclodextrin cavity. Most unusually for a cyclodextrin-based device, the operation of this gate is solvent-independent and unaffected by potentially competitive guests. It occurs in MeOH and DMSO, as well as in water. This contrasts with other cyclodextrin inclusion phenomena that are usually driven by hydrophobic effects and limited to aqueous media.

Harnessing the energy of molecular recognition in a nanomachine having a photochemical on/off switch.

6A-Deoxy-6A-(N-methyl-3-phenylpropionamido)-beta-cyclodextrin operates as a molecular machine, where the amide group serves as a torsion bar to harness the work output resulting from extraction of 1-adamantanol and consequent complexation of the aryl substituent by the cyclodextrin, when the latter behave as the piston and cylinder, respectively, of a molecular pump. At 25 degrees C, the complexation changes the ratio of the amide (Z)- and (E)-isomers from 2.4:1 to 25:1, on which basis the work performed on the amide bond is calculated to be 1.4 kcal mol-1. trans-6A-Deoxy-6A-(N-methylcinnamido)-beta-cyclodextrin and the cis isomer function as a more advanced version of the machine, with the alkene moiety serving as a photochemical on/off switch. Irradiation at 300 nm converts the trans cinnamide to the cis isomer, while the reverse process occurs at 254 nm. With the cis isomer there is little interaction of the phenyl group with the cyclodextrin cavity, so in that mode the machine is turned off. By contrast, complexation of the aryl substituent by the cyclodextrin occurs with the trans cinnamide and changes the ratio of the amide (Z)- and (E)-isomers from 2.6:1 to 100:1. Consequently, in this mode the machine is turned on, and the work harnessed by the amide bond is 2.1 kcal mol-1.

Mechanically regulated rotation of a guest in a nanoscale host.

The spinning rate of an encapsulated cyclophane guest is affected by the "size" of the coguests.

Molecular reactors and machines: applications, potential, and limitations.

Molecular reactors are miniature vessels for the assembly of reactants at the molecular level, in order to change the nature of chemical transformations. It seems probable that those that will find most immediate applications are those that change product ratios or give products which would not readily form in the absence of the reactors, and thereby afford easy access to materials that are otherwise difficult to obtain. Molecular machines consist of interrelated parts with separate functions and perform some kind of work, at the molecular level. Practical examples are likely to be relatively uncomplicated and not based on individual functions of single-molecule devices. Instead they will probably rely on extensive redundancy of the molecular components and their interactions and reactions, as well as of the machines themselves.

Installation of a ratchet tooth and pawl to restrict rotation in a cyclodextrin rotaxane.

Eight new [2]rotaxanes have been prepared, incorporating an alpha-cyclodextrin as the rotor, a stilbene as the axle, and trinitrophenyl substituents as capping groups. Strategies have been devised to elaborate these by linking the rotor to the axle, to produce two new [1]rotaxanes. Rotational motion in a selection of these rotaxanes has been investigated through the application of two-dimensional NMR spectroscopy by performing TOCSY, DQF-COSY, ROESY and HMQC experiments. This has shown that a methoxyl group incorporated on the stilbene and a succinamide joining the stilbene and the cyclodextrin behave analogously to a ratchet tooth and pawl, respectively, to restrict rotation.

Separated and aligned molecular fibres in solid state self-assemblies of cyclodextrin [2]rotaxanes.

The conformations of two [2]rotaxanes, each comprising alpha-cyclodextrin as the rotor, a stilbene as the axle and 2,4,6-trinitrophenyl substituents as the capping groups, have been examined in solution and in the solid state, using (1)H NMR spectroscopy and X-ray crystallography, respectively. In solution, introducing substituents onto the stilbene prevents the cyclodextrin from being localized over one end of the axle. Instead the cyclodextrin moves back and forth along the substituted stilbene. In the solid state, the axles of the rotaxanes form extended molecular fibres that are separated from each other and aligned along a single axis. The molecular fibres are strikingly similar to those formed by the axle component of one of the rotaxanes in the absence of the cyclodextrin, but in the latter case they are neither separated nor all aligned.