Open-chain Form Research Articles

Biochemical communication between filament-forming enzymes: Potential Regulatory Roles of Metabolites in Enzyme Co-assemblies with CTP Synthase.

A host of metabolic enzymes reversibly self-assemble to form membrane-less, intracellular filaments under normal physiological conditions and in response to stress. Often, these enzymes reside at metabolic control points, suggesting that filament formation affords an additional regulatory mechanism. Examples include cytidine-5'-triphosphate (CTP) synthase (CTPS), which catalyzes the rate-limiting step for the de novo biosynthesis of CTP; inosine-5'-monophosphate dehydrogenase (IMPDH), which controls biosynthetic access to guanosine-5'-triphosphate (GTP); and ∆1-pyrroline-5-carboxylate (P5C) synthase (P5CS) that catalyzes the formation of P5C, which links the Krebs cycle, urea cycle, and proline metabolism. Intriguingly, CTPS can exist in co-assemblies with IMPDH or P5CS. Since GTP is an allosteric activator of CTPS, the association of CTPS and IMPDH filaments accords with the need to coordinate pyrimidine and purine biosynthesis. Herein, a hypothesis is presented furnishing a biochemical connection underlying co-assembly of CTPS and P5CS filaments - potent inhibition of CTPS by glutamate γ-semialdehyde, the open-chain form of P5C.

HAuCl4-mediated green synthesis of highly stable Au NPs from natural active polysaccharides: Synthetic mechanism and antioxidant property

Polysaccharide-functionalized gold nanoparticles (Polysaccharide-Au NPs) with high stability were successfully prepared by a straightforward method. Notably, the Au (III) ion acts as a strong Lewis acid to facilitate glycosidic bond breaking. Subsequently, the polysaccharide conformation was transformed to an open-chain form, exposing highly reduced aldehyde or ketone groups that reduce Au (III) to Au (0) crystal species, further growing into Au NPs. As-prepared Au NPs displayed excellent stability over a longer storage period (more than 70 days), a wide range of temperatures (25–60 °C), and pH range (3−11), varying concentrations (0–200 mM) and types of salt ions (Na+, K+, Ca2+, Mg2+), and glutathione solutions (5 mM). More interestingly, polysaccharide-Au NPs retained the antioxidant activity of polysaccharides and reduced oxidative damage at the cellular level through decreased reactive oxygen species (ROS) production. The intracellular levels of ROS pretreated with polysaccharide and polysaccharide-Au NPs were decreased 53.12–75.85 % compared to the H2O2 group, respectively. Therefore, the green synthesized Au NPs from natural active polysaccharides exhibit potential applications in biomedical fields.

Theoretical study on the adsorption and oxidation of glucose on Au(111) surface.

While Au-based catalysts recently have shown tremendous potential in glucose oxidation to gluconic acid, the detailed reaction mechanism is still unclear, which impedes the development of direct glucose fuel cell (DGFC). Using density functional theory (DFT), we exhibit some new adsorption configurations and oxidation mechanisms by considering both the open chain form and the ring form of glucose on Au(111) surface in the presence of OH. The strong interactions between glucose and the OH adsorbed surface are obtained. Moreover, form the calculated energy pathways, the oxidation of glucose in the open chain involves the dissociation of the formyl C - H bond by the adsorbed OH, while the ring form glucose oxidation is initiated by O - H bond rupture rather than C - H bond scission and preferentially undergoes the ring-open process to generate the open chain form glucose. Meanwhile, the results demonstrate that the adsorbed OH assists in reducing the activation energy of reaction process.

P5C as an Interface of Proline Interconvertible Amino Acids and Its Role in Regulation of Cell Survival and Apoptosis.

Studies of cancer metabolism have focused on the production of energy and the interconversion of carbons between cell cycles. More recently, amino acid metabolism, especially non-essential amino acids (NEAAs), has been investigated, underlining their regulatory role. One of the important mediators in energy production and interconversion of carbons in the cell is Δ1-pyrroline-5-carboxylate (P5C)—the physiological intracellular intermediate of the interconversion of proline, ornithine, and glutamate. As a central component of these conversions, it links the tricarboxylic acid cycle (TCA), urea cycle (UC), and proline cycle (PC). P5C has a cyclic structure containing a tertiary nitrogen atom (N) and is in tautomeric equilibrium with the open-chain form of L-glutamate-γ-semialdehyde (GSAL). P5C is produced by P5C synthase (P5CS) from glutamate, and ornithine via ornithine δ-amino acid transferase (δOAT). It can also be converted to glutamate by P5C dehydrogenase (P5CDH). P5C is both a direct precursor of proline and a product of its degradation. The conversion of P5C to proline is catalyzed by P5C reductase (PYCR), while proline to P5C by proline dehydrogenase/oxidase (PRODH/POX). P5C-proline-P5C interconversion forms a functional redox couple. Their transformations are accompanied by the transfer of a reducing-oxidizing potential, that affect the NADP+/NADPH ratio and a wide variety of processes, e.g., the synthesis of phosphoribosyl pyrophosphate (PRPP), and purine ribonucleotides, which are crucial for DNA synthesis. This review focuses on the metabolism of P5C in the cell as an interconversion mediator of proline, glutamate, and ornithine and its role in the regulation of survival and death with particular emphasis on the metabolic context.

Elucidating the effect of solid base on the hydrogenation of C5 and C6 sugars over Pt–Sn bimetallic catalyst at room temperature

Conversion of sugars into sugar alcohols at room temperature with exceedingly high yields are achieved over Pt–Sn/γ-Al2O3 catalyst in the presence of calcined hydrotalcite. pH of the reaction mixture significantly affects the conversion and selectivity for sugar alcohols. Selection of a suitable base is the key to achieve optimum yields. Various solid bases in combination with Pt–Sn/γ-Al2O3 catalysts were evaluated for hydrogenation of sugars. Amongst all combinations, the mixture (1:1 wt/wt) of Pt–Sn/γ-Al2O3 and calcined hydrotalcite showed the best results. Hydrotalcite helps to make the pH of reaction mixture alkaline at which sugar molecules undergo ring opening. The sugar molecule in open chain form has carbonyl group which can be polarized by Sn in Pt–Sn/γ-Al2O3 and Pt facilitates the hydrogenation. In the current work, effect of both; solid base and Sn as a promoter has been studied to improve the yields of sugar alcohols from various C5 and C6 sugars at very mild reaction conditions.

Synthesis of Anemoclemosides A and B, Two Saponins Isolated from Anemoclema glaucifolium

Steroidal and triterpenoid saponins are attractive for their wide‐ranging pharmacological properties. The triterpenoid saponins Anemoclemoside A and B are root constituents of the Chinese folk medicinal plant Anemoclema glaucifolium (Ranunculaceae). Both compounds feature an unusual cyclic acetal linkage to the carbohydrate l‐arabinose in its open chain form rather than the typical glycosidic bond present in normal saponins. The straightforward and scalable syntheses of both saponins starting from l‐arabinose as well as l‐lyxose and l‐rhamnose are described.

Binding of warfarin differently affects the thermal behavior and chain packing of anionic, zwitterionic and cationic lipid membranes

Warfarin is a coumarin derivative drug widely used for its anticoagulant properties. The interaction of warfarin with fully hydrated lipid bilayers has been studied by combining differential scanning calorimetry, spectrophotometry, electron spin resonance of chain-labelled lipids and molecular docking. Bilayers formed by lipids with different chemico-physical properties were considered, namely dimyristoyl-phosphatidylcholine (DMPC), dimyristoyl-phosphatidylglycerol (DMPG), and dioleoyltrimethyl-ammoniumpropane (DOTAP). We observed in all cases the binding of warfarin in proximity of the surface of the bilayers, leading to a variety of distinct effects on key molecular properties of the membranes. The drug associates with the lipid bilayers in the deprotonated open chain form, with an association constant similar for DMPC and DMPG (1.27·104 and 2.82·104 M−1, respectively) and lower for DOTAP (0.46·104 M−1). In DMPC bilayers, which are zwitterionic and with saturated symmetrical chains, warfarin at 10 mol% suppresses the pre-transition, slightly stabilizes the fluid state and reduces the cooperativity of the main transition. Moreover, it alters the lateral packing density of the chain segments close to the polar/apolar interface at any temperature through the gel phase. In anionic DMPG bilayers, the drug slightly perturbs the thermotropic phase behavior, and at 10 mol% markedly loosens the compact gel phase packing of the first chain segments. In cationic DOTAP bilayers, possessing unsaturated acyl chains, the drug induces a slightly higher degree of order and motional restriction in the outer hydrocarbon region in the frozen state. In all cases, as a surface adsorbed molecule, warfarin does not affect the segmental chain order and dynamics for temperatures in the fluid phase. The overall results provide an outline of the action of warfarin on membranes formed by lipids of different types.

Carbocyclic Substrate Analogues Reveal Kanosamine Biosynthesis Begins with the α-Anomer of Glucose 6-Phosphate.

NtdC is an NAD-dependent dehydrogenase that catalyzes the conversion of glucose 6-phosphate (G6P) to 3-oxo-glucose 6-phosphate (3oG6P), the first step in kanosamine biosynthesis in Bacillus subtilis and other closely-related bacteria. The NtdC-catalyzed reaction is unusual because 3oG6P undergoes rapid ring opening, resulting in a 1,3-dicarbonyl compound that is inherently unstable due to enolate formation. We have reported the steady-state kinetic behavior of NtdC, but many questions remain about the nature of this reaction, including whether it is the α-anomer, β-anomer, or open-chain form that is the substrate for the enzyme. Here, we report the synthesis of carbocyclic G6P analogues by two routes, one based upon the Ferrier II rearrangement to generate the carbocycle and one based upon a Claisen rearrangement. We were able to synthesize both pseudo-anomers of carbaglucose 6-phosphate (C6P) using the Ferrier approach, and activity assays revealed that the pseudo-α-anomer is a good substrate for NtdC, while the pseudo-β-anomer and the open-chain analogue, sorbitol 6-phosphate (S6P), are not substrates. A more efficient synthesis of α-C6P was achieved using the Claisen rearrangement approach, which allowed for a thorough evaluation of the NtdC-catalyzed oxidation of α-C6P. The requirement for the α-anomer indicates that NtdC and NtdA, the subsequent enzyme in the pathway, have co-evolved to recognize the α-anomer in order to avoid mutarotation between enzymatic steps.

Mutarotation of aldoses: Getting a deeper knowledge of a classic equilibrium enabled by computational analyses

The mutarotation equilibrium, by which reducing carbohydrates exist in solution as the α and β anomers of cyclic (furanoid and pyranoid) structures, along with open-chain (aldehyde and hydrate) forms, and whose ratios are depending on factors such as temperature, pH and solvent, portraits a phenomenon involved in numerous processes of chemical and biological importance. Herein, we have developed a DFT-based rationale that provides a broader landscape for anomerizations and ring-open chain interconversions, together with the pivotal role exerted not only by the aldehyde intermediate (essentially the only acyclic structure taken into account so far), but also the hydrate form (often more abundant at the equilibrium). These calculations reveal a more complex and richer scenario than was thought, and identify different mutarotation mechanisms that hinge on every monosaccharide. It is noteworthy that pyranose-furanose interconversion may actually occur without the intermediacy of open-chain forms. For the aldoses evaluated, namely d-glucose, d-ribose, and d-xylose, all structures involved in mutarotation undergo interconversion pathways, whose energy barriers calculated at the M06-2X/6-311++G(d,p) level, are in good agreement with previous experimental measurements.

Structure and mechanism of piperideine-6-carboxylate dehydrogenase from Streptomyces clavuligerus.

The core of β-lactam antibiotics originates from amino acids of primary metabolism in certain microorganisms. β-Lactam-producing bacteria, including Streptomyces clavuligerus, synthesize the precursor of the amino acid α-aminoadipic acid by the catabolism of lysine in two steps. The second reaction, the oxidation of piperideine-6-carboxylate (or its open-chain form α-aminoadipate semialdehyde) to α-aminoadipic acid, is catalysed by the NAD+-dependent enzyme piperideine-6-carboxylate dehydrogenase (P6CDH). This structural study, focused on ligand binding and catalysis, presents structures of P6CDH from S. clavuligerus in its apo form and in complexes with the cofactor NAD+, the product α-aminoadipic acid and a substrate analogue, picolinic acid. P6CDH adopts the common aldehyde dehydrogenase fold, consisting of NAD-binding, catalytic and oligomerization domains. The product binds in the oxyanion hole, close to the catalytic residue Cys299. Clear density is observed for the entire cofactor, including the nicotinamide riboside, in the binary complex. NAD+ binds in an extended conformation with its nicotinamide ring overlapping with the binding site of the carboxylate group of the product, implying that the conformation of the cofactor may change during catalysis. The binding site of the substrate analogue overlaps with that of the product, suggesting that the cyclic form of the substrate, piperideine-6-carboxylate, may be accepted as a substrate by the enzyme. The catalytic mechanism and the roles of individual residues are discussed in light of these results.

Elucidating Peptidoglycan Structure: An Analytical Toolset.

Peptidoglycan (PG) is a ubiquitous structural polysaccharide of the bacterial cell wall, essential in preserving cell integrity by withstanding turgor pressure. Any change that affects its biosynthesis or degradation will disturb cell viability, therefore PG is one of the main targets of antimicrobial drugs. Considering its major role in cell structure and integrity, the study of PG is of utmost relevance, with prospective ramifications to several disciplines such as microbiology, pharmacology, agriculture, and pathogenesis. Traditionally, high-performance liquid chromatography (HPLC) has been the workhorse of PG analysis. In recent years, technological and bioinformatic developments have upgraded this seminal technique, making analysis more sensitive and efficient than ever before. Here we describe a set of analytical tools for the study of PG structure (from composition to 3D architecture), identify the most recent trends, and discuss future challenges in the field.

Synthesis, structure and catalytic activity of novel five-membered Pd(II) and Pt(II) metallaheterocycles based on 1,2-bis(3,5-dimethylisoxazol-4-yl-methylsulfanyl)ethane

Novel palladium(II) and platinum(II) heterocycles were synthesized based 1,2-bis(3,5-dimethylisoxazol-4-ylmethylsulfanyl)ethane. According to X-ray Crystallographic data in molecule there are two bonds between divalent sulfur atoms and metal atom S-Pd-S to form a five-membered palladacycle in the twist-conformation with trans orientation of isoxazole rings. The syn-anti-isomerization for the palladaheterocycle in the solution is observed. The activation energy ΔH≠, ΔS≠ and rate of reversible syn-anti-isomerization were established by the dynamic 1H NMR method and quantum-chemical calculations. Proposed mechanism of syn-anti-isomerization of palladacycle via an open-chain forms was offered. It was shown that metallaheterocycle - cis-S,S-dichloro 1,2-[di-(3,5-dimethylisoxazol-4-yl)methylsulfanyl]ethane palladium(II) is efficient catalyst in the amination reaction of allyl phenyl ether and Sonogashira reaction.

Intramolecular [4+2] cycloaddition in N-allyl- and N-propargyl-α-furyl lactams

The size of nitrogen heterocycle in N-allyl- and N-propargyl-α-furyl lactams, as well as the nature of the unsaturated substituent linked to the nitrogen atom affected the possibility of thermal intramolecular [4+2] cycloaddition between multiple bond and the furan ring. N-Allyl-γ-(α-furyl)butyrolactam was shown to be unreactive at temperatures from 140 to 230°С. Substituted δ-valero- and e-caprolactams underwent partial Diels–Alder cyclization, forming tautomeric mixtures that contained both the initial open-chain form and the cyclic form (diastereomeric 3a,6-epoxyisoindoles fused with an aza ring) in ratios between 19:81 and 55:45. N-Propargyl-α-furyl lactams did not participate in thermal IMDAF reaction regardless of the ring size and the temperature of the synthesis.

Oxadiazole-substituted naphtho[2,3-b]thiophene-4,9-diones as potent inhibitors of keratinocyte hyperproliferation. Structure−activity relationships of the tricyclic quinone skeleton and the oxadiazole substituent

Novel analogues of oxadiazole-substituted naphtho[2,3-b]thiophene-4,9-diones were synthesized in which the tricyclic quinone skeleton was systematically replaced with simpler moieties, such as structures with fewer rings and open-chain forms, while the oxadiazole ring was maintained. In addition, variants of the original 1,2,4-oxadiazole ring were explored. Overall, the complete three-ring quinone was essential for potent suppression of human keratinocyte hyperproliferation, whereas analogous anthraquinones were inactive. Also, the oxadiazole ring per se was not sufficient to elicit activity. However, rearrangement of the heteroatom positions in the oxadiazole ring resulted in highly potent inhibitors with compound 24b being the most potent analogue of this series showing an IC50 in the nanomolar range. Furthermore, experiments in isolated enzymatic assays as well as in the keratinocyte-based hyperproliferation assay did not support a major role of redox cycling in the mode of action of the compounds.

Mystery of 1-Vinylpropargyl Formation from Acetylene Addition to the Propargyl Radical: An Open-and-Shut Case.

The addition of acetylene (C2H2) to the propargyl radical (C3H3) initiates a cascade of molecular weight growth reactions that result in the production of polycyclic aromatic hydrocarbons (PAHs) in flames. Although it is well-established that the first reaction step produces the cyclic C5H5 radical cyclopentadienyl (c-C5H5), recent studies have also detected significant quantities of the open-chain form, 1-vinylpropargyl (l-C5H5). This work presents a mechanism for the C3H3 + C2H2 reaction from ab initio calculations, which includes pathways for the formation of both the open and shut isomers as well as for their interconversion. Formation of both isomers proceeds from the initial HCCCH2CHCH• reaction adduct with similar barriers, both well below the entrance channel energy. Subsequent isomerization of l-C5H5 with c-C5H5 also transpires at below the energy of the reactants, although this process connects two deep wells (being resonance stabilized radicals), and must compete with collisional energy transfer. An RRKM theory/master equation model is developed for the reported C5H5 reaction mechanism. Master equation simulations suggest that both cyclic and open-chain isomers are expected to form from the C3H3 + C2H2 reaction across a range of temperatures, although the lifetime of l-C5H5 is relatively short for rearrangement to c-C5H5.

Alternative Route Toward Nitrones: Experimental and Theoretical Findings.

Nitrones are important building blocks for natural and biologically active compounds, used as spin-trap reagents and therapeutic agents. All this makes nitrones intriguing and valuable compounds for fundamental studies and as useful chemicals in various synthetic strategies. Therefore, nitrones are still of great interest and in the limelight of researches. With our initial goal to solve synthetic problems toward 5-phenyl-2,2'-bipyridine (Phbpy), we found that this reaction can proceed through the formation of 6-phenyl-3-(pyridin-2-yl)-1,2,4-triazin-4(3H)-ol (4-OH), which rapidly isomerizes to a 3,4-dihydro-1,2,4-triazine-based nitrone, namely 6-phenyl-3-pyridin-2-yl-2,3-dihydro-1,2,4-triazin-4-oxide (4'), This encouraged us to study condensation of hydrazonophenylacetaldehyde oxime (2), obtained from 2-isonitrosoacetophenone (1), with other aldehydes. The reaction with both salicylaldehyde and p-tolualdehyde leads to the open-chain isomers, namely (2-hydroxybenzylidene)hydrazono-2-phenylacetaldehyde oxime (5) and (4-methylbenzylidene)hydrazono-2-phenylacetaldehyde oxime (6), respectively. The latter product exists in solution in equilibrium with its cyclic isomer 6-phenyl-3-(4-methylphenyl)-2,3-dihydro-1,2,4-triazin-4-oxide (6'), while the former one exists in solution exclusively in the open-chain form. It was also found that 2 reacts with acetone with the formation of 3,3-dimethyl-6-phenyl-2,3-dihydro-1,2,4-triazin-4-oxide (7'), which also exists in solution in equilibrium with its open-chain isomer 2-phenyl-2-(propan-2-ylidenehydrazono)acetaldehyde oxime (7). The static DFT as well as ab initio molecular dynamics simulations have corroborated the experimental findings.

Dynamic Exchange in Intramolecular Lewis Pairs with Multiple Lewis-Acidic Functions

Hydroboration of allyldimethylamine, diallylmethylamine, triallylamine, and diallylmethylphosphane with dimeric 9-BBN yielded the corresponding singly, doubly, and triply Lewis-acid-functionalized intramolecular Lewis pairs. For the singly Lewis-acid-functionalized derivative Me2N(CH2)3-9-BBN no evidence for the existence of an equilibrium involving an open-chain form was found in solution. For the doubly and triply Lewis-acid-functionalized compounds Me3–xE[(CH2)3-9-BBN]x [E = N (x = 2, 3), P (x = 2)] a dynamic exchange of the free Lewis-acid functions with an intramolecular Lewis acid base complex was observed and investigated by variable-temperature NMR spectroscopy. The free energies of activation of the exchange processes were determined by the coalescence method and found to be lower for the Lewis-base component nitrogen than for phosphorus. To further understand the exchange process of the Lewis acids at the central Lewis base, transition states for two different exchange mechanisms were considered...

Synthesis of 1,4,6,10-tetraazaadamantane quaternary derivatives

Methods for the preparation of stable 1,4,6,10-tetraazaadamantane quaternary derivatives were developed based on quaternization of a tertiary nitrogen atom in tris(β-oximinoalkyl)amines or isomeric 4,6,10-trihydroxy-1,4,6,10-tetraazaadamantanes. This process constitutes a convenient approach to the introduction of a hydrophilic 1,4,6,10-tetraazaadamantane moiety into lipophilic molecules in order to increase their solubility in water. 4,6,10-Trihydroxy-1,4,6,10-tetraazaadamantane N-oxide was synthesized by the oxidation of the tertiary nitrogen atom in the tris-oxime and subsequent intramolecular cyclotrimerization of the oximino groups. Quantum chemical calculations showed that the quaternization of the annular nitrogen atom led to a considerable stabilization of tetraazaadamantane framework as compared to the open-chain form of tris-oxime.

Selective transformation of tricyclic peroxides with pronounced antischistosomal activity into 2-hydroxy-1,5-diketones using iron (II) salts

The present work deals with selective transformations of peroxides into organic compounds via the cleavage of the O–O bond using variable valence metals. A selective transformation of tricyclic peroxides promoted by Fe2+ salts was discovered. This selective transformation is unexpected for compounds with structural features which allow diverse decomposition pathways. 2-Hydroxy-1,5-diketones are prepared in yields up to 92% in the reactions of tricyclic peroxides with FeSO4, Fe(ClO4)2, or FeCl2. This is a new preparative method for the synthesis of 1,5-diketones. 2-Hydroxy-1,5-diketones in CDCl3 at 25 °C exist mainly in the open-chain form of the hydroxyketone over the cyclic hemiacetal. The results of this work can be of interest to understand the mechanism of the antiparasitic action of peroxides.

Novel mode of inhibition by D-tagatose 6-phosphate through a Heyns rearrangement in the active site of transaldolase B variants.

Transaldolase B (TalB) and D-fructose-6-phosphate aldolase A (FSAA) from Escherichia coli are C-C bond-forming enzymes. Using kinetic inhibition studies and mass spectrometry, it is shown that enzyme variants of FSAA and TalB that exhibit D-fructose-6-phosphate aldolase activity are inhibited covalently and irreversibly by D-tagatose 6-phosphate (D-T6P), whereas no inhibition was observed for wild-type transaldolase B from E. coli. The crystal structure of the variant TalB(F178Y) with bound sugar phosphate was solved to a resolution of 1.46 Å and revealed a novel mode of covalent inhibition. The sugar is bound covalently via its C2 atom to the ℇ-NH2 group of the active-site residue Lys132. It is neither bound in the open-chain form nor as the closed-ring form of D-T6P, but has been converted to β-D-galactofuranose 6-phosphate (D-G6P), a five-membered ring structure. The furanose ring of the covalent adduct is formed via a Heyns rearrangement and subsequent hemiacetal formation. This reaction is facilitated by Tyr178, which is proposed to act as acid-base catalyst. The crystal structure of the inhibitor complex is compared with the structure of the Schiff-base intermediate of TalB(E96Q) formed with the substrate D-fructose 6-phosphate determined to a resolution of 2.20 Å. This comparison highlights the differences in stereochemistry at the C4 atom of the ligand as an essential determinant for the formation of the inhibitor adduct in the active site of the enzyme.