Probing the Subunit-Subunit Interaction of the Tetramer of E. coli KDO8P Synthase by Electrospray Ionization Mass Spectrometry

Escherichia coli 3-Deoxy-D-manno-octulosonate 8-phosphate (KDO8P) synthase catalyzes the condensation reaction between D-arabinose 5-phosphate (A5P) and phosphoenolpyruvate (PEP) to form KDO8P and inorganic phosphate (Pi). This enzyme exists as a tetramer in solution, which is important for catalysis. Two different states of the enzyme were obtained: i) PEP-bound and ii) PEP-unbound. The effect of the substrates and products on the overall structure of KDO8P synthase in both PEP-bound and unbound states was examined using electrospray ionization mass spectrometry. The analysis of our data showed that the complexes of the PEP-unbound enzyme with PEP (or Pi) favored the formation of monomers, while the complexes with A5P (or KDO8P) mainly favored dimers. The PEP-bound enzyme was found to exist in the monomer and dimer with a small amount of the tetramer, whereas the PEP-unbound form primarily exists in the monomer and dimer, and no tetramer was observed, suggesting that the bound PEP have a role in stabilization of the tetrameric structure. Taken together, the results imply that the addition of the substrates or products to the unbound enzyme may alter the subunit-subunit interactions and/or conformational change of the protein at the active site, and this study also demonstrates that the electrospray ionization mass spectrometric method may be a powerful tool in probing the subunit-subunit interactions and/or conformational change of multi-subunit protein upon binding to ligand.     

Observation of a chemically labile,noncovalent enzyme intermediate in the reaction of metal‐dependent Aquifex pyrophilus KDO8PS by time‐resolved mass spectrometry

The direct detection of intermediates in enzymatic reactions can yield important mechanistic insights but may be difficult due to short intermediate lifetimes and chemical instability. Using a rapid‐mixing device coupled with electrospray ionization time‐of‐flight mass spectrometry, the noncovalent hemiketal intermediate in the reaction of metal‐dependent 3‐deoxy‐D‐manno‐octulosonate‐8‐phosphate (KDO8P) synthase from Aquifex pyrophilus was observed in the millisecond time range. Using single turnover conditions, the noncovalent complexes of enzyme with Cd²⁺:phosphoenolpyruvate, Cd²⁺:phosphate, Cd²⁺:KDO8P, and Cd²⁺:intermediate complexes were resolved. The intermediate complex is present during times ranging from 50–630 ms, indicating that the intermediate builds up at the ambient temperatures of the experiment. This represents the first direct detection of the intermediate with a native metal‐dependent KDO8PS, and further demonstrates that time‐resolved mass spectrometry is a useful tool in mechanistic studies of enzymatic reactions. Copyright © 2010 John Wiley & Sons, Ltd.     

Inhibitors of the Bifunctional 2‐C‐Methyl‐d‐erythritol 4‐Phosphate Cytidylyl Transferase/2‐C‐Methyl‐d‐erythritol‐2,4‐cyclopyrophosphate Synthase (IspDF) of Helicobacter pylori

A library of over 103 thousand compounds was screened for inhibitors of the IspD domain (2‐C‐methyl‐d ‐erythritol 4‐phosphate cytidylyl transferase domain) of the bifunctional IspDF protein from Helicobacter pylori using a photometric assay. Around 300 compounds showed IC₅₀ values below 100 μm , and three compounds had IC₅₀ values below 1 μm . A few IspD inhibitors could also inhibit the IspF domain (2‐C‐Methyl‐d ‐erythritol‐2,4‐cyclopyrophosphate synthase) of the IspDF protein. The most potent IspD inhibitors were tested as growth inhibitors of H. pylori. Several compounds showed inhibition of bacterial growth with IC₅₀ in the single‐digit μm range. The most potent growth inhibitor had an IC₅₀ value of 3.4 μm . The most potent growth inhibitor without measurable effect on eukaryotic cell viability had an IC₅₀ value of 7.2 μm .     

Chiral discrimination of β‐3‐homo‐amino acids using the kinetic method

Chiral discrimination of seven enantiomeric pairs of β‐3‐homo‐amino acids was studied by using the kinetic method and trimeric metal‐bound complexes, with natural and unnatural α‐amino acids as chiral reference compounds and divalent metal ions (Cu²⁺ and Ni²⁺) as the center ions. The β‐3‐homo‐amino acids were selected for this study because, first of all, chiral discrimination of β‐amino acids has not been extensively studied by mass spectrometry. Moreover, these β‐3‐homo‐amino acids studied have different aromatic side chains. Thus, the emphasis was to study the effect of the side chain (electron density of the phenyl ring, as well as the difference between phenyl and benzyl side chains) for the chiral discrimination. The results showed that by the proper choice of a metal ion and a chiral reference compound, all seven enantiomeric pairs of β‐3‐homo‐amino acids could be differentiated. Moreover, it was noted that the β‐3‐homo‐amino acids with benzyl side chains provided higher enantioselectivity than the corresponding phenyl ones. However, increasing or decreasing the electron density of the aromatic ring by different substituents in both the phenyl and benzyl side chains had practically no role for chiral discrimination of β‐3‐homo‐amino acids studied. When copper was used as the central metal, the phenyl side chain containing reference molecules (S)‐2‐amino‐2‐phenylacetic acid (L ‐Phg) and (S)‐2‐amino‐2‐(4‐hydroxyphenyl)‐acetic acid (L ‐4′‐OHPhg) gave rise to an additional copper‐reduced dimeric fragment ion, [Cu^I(ref)(A)]⁺. The inclusion of this ion improved noticeably the enantioselectivity values obtained. Copyright © 2010 John Wiley & Sons, Ltd.     

Metal‐Ion‐Mediated Tuning of Duplex DNA Binding by Bis(2‐(2‐pyridyl)‐1H‐benzimidazole)

Studies of double‐stranded‐DNA binding have been performed with three isomeric bis(2‐(n‐pyridyl)‐1H‐benzimidazole)s (n=2, 3, 4). Like the well‐known Hoechst 33258, which is a bisbenzimidazole compound, these three isomers bind to the minor groove of duplex DNA. DNA binding by the three isomers was investigated in the presence of the divalent metal ions Mg²⁺, Co²⁺, Ni²⁺, Cu²⁺, and Zn²⁺. Ligand–DNA interactions were probed with fluorescence and circular dichroism spectroscopy. These studies revealed that the binding of the 2‐pyridyl derivative to DNA is dramatically reduced in the presence of Co²⁺, Ni²⁺, and Cu²⁺ ions and is abolished completely at a ligand/metal‐cation ratio of 1:1. Control experiments done with the isomeric 3‐ and 4‐pyridyl derivatives showed that their binding to DNA is unaffected by the aforementioned transition‐metal ions. The ability of 2‐(2‐pyridyl)benzimidazole to chelate metal ions and the conformational changes of the ligand associated with ion chelation probably led to such unusual binding results for the ortho isomer. The addition of ethylenediaminetetraacetic acid (EDTA) reversed the effects completely.     

Tautomeric Switching and Metal‐Cation Sensing of Ligand‐Equipped 4‐Hydroxy‐/4‐oxo‐1,4‐dihydroquinolines

Novel 4‐hydroxyquinoline (4HQ) based tautomeric switches are reported. 4HQs equipped with coordinative side arms (8‐arylimino and 3‐piperidin‐1‐ylmethyl groups) were synthesized to access O‐ or N‐selective chelation of Zn²⁺ and Cd²⁺ ions by 4HQ. In the case of the monodentate arylimino group, O chelation of metal ions induces concomitant switching of phenol tautomer to the keto form in nonpolar or aprotic media. This change is accompanied by selective and highly sensitive fluorometric sensing of Zn²⁺ ions. In the case of the bidentate 8‐(quinolin‐8‐ylimino)methyl side arm, NMR studies in CD₃OD indicated that both Cd²⁺ and Zn²⁺ ions afford N chelation for 4HQ, coexisting with tautomeric switching from quinolin‐4(1H)‐one to quinolin‐4‐olate. In corroboration, UV/Vis‐monitored metal‐ion titrations in toluene and methanol implied similar structural changes. Additionally, fluorescence measurements indicated that the metal‐triggered tautomeric switching is associated with compound signaling properties. The results are supported by DFT calculations at the B3LYP 6‐31G* level. Several X‐ray structures of metal‐free and metal‐chelating 4HQ are presented to support the solution studies.     

Competitive heavy metal removal by poly(2‐acrylamido‐2‐methyl‐1‐propane sulfonic acid‐co‐itaconic acid)

The competitive removal of Pb²⁺, Cu²⁺, and Cd²⁺ ions from aqueous solutions by the copolymer of 2‐acrylamido‐2‐methyl‐1‐propane sulfonic acid (AMPS) and itaconic acid (IA), P(AMPS‐co‐IA), was investigated. Homopolymer of AMPS (PAMPS) was also used to remove these ions from their aqueous solution. In the preparation of AMPS–IA copolymer, the molar percentages of AMPS and IA were 80 and 20, respectively. In order to observe the changes in the structures of polymers due to metal adsorption, FTIR spectra by attenuated total reflectancetechnique and scanning electron microscopy (SEM) pictures of the polymers were taken both before and after adsorption experiments. Total metal ion removal capacities of PAMPS and P(AMPS‐co‐IA) were 1.685 and 1.722 mmol Me²⁺/g_polymer, respectively. Experimental data were evaluated to determine the kinetic characteristics of the adsorption process. Competitive adsorption of Pb²⁺, Cu²⁺, and Cd²⁺ ions onto both PAMPS and P(AMPS‐co‐IA) was found to fit pseudo‐second‐order type kinetics. In addition, the removal orders in the competitive adsorption of these metal ions onto PAMPS and P(AMPS‐co‐IA) were found to be Cd²⁺ > Pb²⁺ > Cu²⁺ and Pb²⁺ > Cd²⁺ > Cu²⁺, respectively. Copyright © 2008 John Wiley & Sons, Ltd.     

An Improved Preparation of D‐Glyceraldehyde 3‐Phosphate and Its Use in the Synthesis of 1‐Deoxy‐D‐xylulose 5‐Phosphate

D ‐Glyceraldehyde 3‐phosphate (=D ‐GAP; 2 ) was prepared by an improved chemical method (Scheme 2), and it was then employed to synthesize 1‐deoxy‐D ‐xylulose 5‐phosphate (=DXP; 3 ) which is enzymatically one of the key intermediates in the MEP ( 4 ) terpenoid biosynthetic pathway (Scheme 1). The recombinant DXP synthase of Rhodobacter capsulatus was used to catalyze the condensation of D ‐glyceraldehyde 3‐phosphate ( 2 ) and pyruvate (=2‐oxopropanoate; 1 ) to produce the sugar phosphate 3 (Scheme 2). The simple two‐step chemoenzymatic route described affords DXP ( 3 ) with more than 70% overall yield and higher than 95% purity. The procedure may also be used for the synthesis of isotope‐labeled DXP ( 3 ) by using isotope‐labeled pyruvate.     

A Dinuclear Mercury(II)‐Mediated Base Pair in DNA

The first dinuclear metal‐mediated base pair containing divalent metal ions has been prepared. A combination of the neutral bis(monodentate) purine derivative 1,N⁶‐ethenoadenine (ϵA), which preferentially binds two metal ions with a parallel alignment of the N−M bonds, and the canonical nucleobase thymine (T), which readily deprotonates in the presence of Hg^II and thereby partially compensates the charge accumulation due to the two closely spaced divalent metal ions, yields the dinuclear T‐Hg^II₂‐ϵA base pair. This metal‐mediated base pair stabilizes the DNA oligonucleotide duplex as shown by an increase of 8 °C in its melting temperature. Formation of the base pair was demonstrated by temperature‐dependent UV spectroscopy as well as by titration experiments monitored by UV and CD spectroscopy.     

Amphiphilic Schiff Base Organogels: Metal‐Ion‐Mediated Chiral Twists and Chiral Recognition

New amphiphilic gelators that contained both Schiff base and L ‐glutamide moieties, abbreviated as o‐SLG and p‐SLG, were synthesized and their self‐assembly in various organic solvents in the absence and presence of metal ions was investigated. Gelation test revealed that o‐SLG formed a thermotropic gel in many organic solvents, whilst p‐SLG did not. When metal ions, such as Cu²⁺, Zn²⁺, Mg²⁺, Ni²⁺, were added, different behaviors were observed. The addition of Cu²⁺ induced p‐SLG to from an organogel. In the case of o‐SLG, the addition of Cu²⁺ and Mg²⁺ ions maintained the gelating ability of the compound, whilst Zn²⁺ and Ni²⁺ ions destroyed the gel. In addition, the introduction of Cu²⁺ ions caused the nanofiber gel to perform a chiral twist, whilst the Mg²⁺ ions enhanced the fluorescence of the gel. More interestingly, the Mg²⁺‐ion‐mediated organogel showed differences in the fluorescence quenching by D ‐ and L ‐tartaric acid, thus showing a chiral recognition ability.     

Chemical Synthesis and Immunological Evaluation of Helicobacter pylori Serotype O6 Tridecasaccharide O‐Antigen Containing a dd‐Heptoglycan

The development of glycoconjugate vaccines against Helicobacter pylori is challenging. An exact epitope of the H. pylori lipo‐polysaccharide (LPS) O‐antigens that contain Lewis determinant oligosaccharides and unique dd ‐heptoglycans has not yet been identified. Reported here is the first total synthesis of H. pylori serotype O6 tridecasaccharide O‐antigen containing a terminal Le^y tetrasaccharide, a unique α‐(1→3)‐, α‐(1→6)‐, and α‐(1→2)‐linked heptoglycan, and a β‐d ‐galactose connector, by an [(2×1)+(3+8)] assembly sequence. Seven oligosaccharides covering different portions of the entire O‐antigen were prepared for immunological investigations with a particular focus on elucidation of the roles of the dd ‐heptoglycan and Le^y tetrasaccharide. Glycan microarray analysis of sera from rabbits immunized with isolated serotype O6 LPS revealed a humoral immune response to the α‐(1→3)‐linked heptoglycan, a key motif for designing glycoconjugate vaccines for H. pylori serotype O6.     

Octamethyl‐1, 1′‐di(2‐pyridyl)ferrocene: A Redox‐Active Ligand with a Pronounced Selectivity for Divalent Metal Ions

Octamethyl‐1, 1′‐di(2‐pyridyl)ferrocene ( 1 ) acts as molecular electrochemical sensor for magnesium, calcium, zinc, and cadmium ions in acetonitrile solution. The new redox peak, anodically shifted by ca. 0.40 V, which appears in the cyclic voltammogram of 1 in the presence of even small amounts (10 mol %) of these ions, is unaffected by an excess of alkali metal ions. Metal complexation is accompanied by a batho‐ and hyper‐chromic shift of the band in the visible region of the UV‐Vis spectrum of 1 . A detailed study of the behaviour of 1 towards zinc chloride in acetonitrile solution has revealed that 1 is able to accommodate a maximum of two zinc ions. Oxidation of zinc‐coordinated 1 leads to partial decomplexation. The N‐methyl and N‐benzyl species 1 Me⁺, 1 Me₂²⁺, 1 Bzl⁺ and 1 Bzl₂²⁺ have been synthesized and the former two structurally investigated by X‐ray diffraction. Alkylation causes an anodic shift of the redox potential of the ferrocene nucleus, which is linearly dependent on the number of alkyl groups introduced. Octamethyl‐1, 1′‐di(2‐thiophenyl)ferrocene ( 2 ) has also been synthesized and structurally characterized by X‐ray diffraction. Cyclic voltammetry has revealed that, in contrast to 1 , 2 does not respond to the divalent metal ions studied.     

Syntheses,structures of N‐(substituted)‐2‐aza‐[3]‐ferrocenophanes and their application as redox sensor for Cu2+ ion

Rigid N‐(substituted)‐2‐aza‐[3]‐ferrocenophanes L1 and L2 were easily synthesized from 1,1 ‐dicarboxyaldehydeferrocene and the corresponding amines. Ligands L1 and L2 were characterized by ¹H NMR, ¹³C NMR and single‐crystal X‐ray crystallography. The coordination abilities of L1 and L2 with metal ions such as Cu²⁺, Mg²⁺, Ni²⁺, Zn²⁺, Pb²⁺ and Cd²⁺ were evaluated by cyclic voltammetry. The electrochemical shift (ΔE_1/2) of 125 mV was observed in the presence of Cu²⁺ ion, while no significant shift of the Fc/Fc + couple was observed when Mg²⁺, Ni²⁺, Zn²⁺, Pb²⁺, Cd²⁺ metal ions were added to the solution of L1 in the mixture of MeOH and H₂O. Moreover, the extent of the anodic shift of redox potentials was approximately equal to that induced by Cu²⁺ alone when a mixture of Cu²⁺, Mg²⁺, Ni²⁺, Zn²⁺, Pb²⁺ and Cd²⁺ was added to a solution of L1. Ligand L1 was proved to selectively sense Cu²⁺ in the presence of large, excessive first‐row transition and late‐transition metal cations. The coordination model was proposed from the results of controlled experiments and quantum calculations. Copyright © 2012 John Wiley & Sons, Ltd.     

9‐Benzylidene‐9H‐fluorene Derivatives Linked to Monoaza‐15‐crown‐5: Synthesis and Metal Ion Sensing

Two kinds of novel styryl chemosensory 2‐FMNC and 3‐FMNC, were designed and synthesized by an apporiate introduction of 9‐benzylidene‐9H‐fluorene group as fluorophore with the aim at avoiding photoisomerisation. These 9‐benzylidene‐9H‐fluorene derivatives showed the similar selectivity and sensitivity upon addition of metal ions. The sensitivity of FMNC to alkaline earth metal ions was Ba²⁺>Sr²⁺>Ca²⁺≈Mg²⁺.     

Polymorph‐Dependent Solid‐State Fluorescence and Selective Metal‐Ion‐Sensor Properties of 2‐(2‐Hydroxyphenyl)‐4(3H)‐quinazolinone

2‐(2‐Hydroxy‐phenyl)‐4(3H)‐quinazolinone (HPQ), an organic fluorescent material that exhibits fluorescence by the excited‐state intramolecular proton‐transfer (ESIPT) mechanism, forms two different polymorphs in tetrahydrofuran. The conformational twist between the phenyl and quinazolinone rings of HPQ leads to different molecular packing in the solid state, giving structures that show solid‐state fluorescence at 497 and 511 nm. HPQ also shows intense fluorescence in dimethyl formamide (DMF) solution and selectively detects Zn²⁺ and Cd²⁺ ions at micromolar concentrations in DMF. Importantly, HPQ not only detects Zn²⁺ and Cd²⁺ ions selectively, but it also distinguishes between the metal ions with a fluorescence λ_max that is blue‐shifted from 497 to 420 and 426 nm for Zn²⁺ and Cd²⁺ ions, respectively. Hence, tunable solid‐state fluorescence and selective metal‐ion‐sensor properties were demonstrated in a single organic material.     

A three‐dimensional homochiral metal–organic framework constructed from manganese(II) with S‐carboxymethyl‐N‐(p‐tosyl)‐l‐cysteine and 4,4′‐bipyridine

In the chiral polymeric title compound, poly[aqua(4,4′‐bipyridine)[μ₃‐S‐carboxylatomethyl‐N‐(p‐tosyl)‐l ‐cysteinato]manganese(II)], [Mn(C₁₂H₁₃NO₆S₂)(C₁₀H₈N₂)(H₂O)]_n, the Mn^II ion is coordinated in a distorted octahedral geometry by one water molecule, three carboxylate O atoms from three S‐carboxyatomethyl‐N‐(p‐tosyl)‐l ‐cysteinate (Ts‐cmc) ligands and two N atoms from two 4,4′‐bipyridine molecules. Each Ts‐cmc ligand behaves as a chiral μ₃‐linker connecting three Mn^II ions. The two‐dimensional frameworks thus formed are further connected by 4,4′‐bipyridine ligands into a three‐dimensional homochiral metal–organic framework. This is a rare case of a homochiral metal–organic framework with a flexible chiral ligand as linker, and this result demonstrates the important role of noncovalent interactions in stabilizing such assemblies.     

7‐Iodo‐5‐aza‐7‐deazaguanine: Syntheses of Anomeric D‐ and L‐Configured 2‐Deoxyribonucleosides

Iodination of N²‐isobutyryl‐5‐aza‐7‐deazaguanine ( 7 ) with N‐iodosuccinimide (NIS) gave 7‐iodo‐N²‐isobutyryl‐5‐aza‐7‐deazaguanine ( 8 ) in a regioselective reaction (Scheme 1). Nucleobase‐anion glycosylation of 8 with 2‐deoxy‐3,5‐di‐O‐toluoyl‐α‐D ‐ or α‐L ‐erythro‐pentofuranosyl chloride furnished anomeric mixtures of D ‐ and L ‐nucleosides. The anomeric D ‐nucleosides were separated by crystallization to give the α‐D ‐anomer and β‐D ‐anomer with excellent optical purity. Deprotection gave the 7‐iodo‐5‐aza‐7‐deazaguanine 2′‐deoxyribonucleosides 3 (β‐D ; ≥99% de) and 4 (α‐D ; ≥99% de). The reaction sequence performed with the D ‐series was also applied to L ‐nucleosides to furnish compounds 5 (β‐L ; ≥99% de) and 6 (α‐L ; ≥95% de).     

Di­aqua­tetrakis­(pyridine‐2,6‐di­carbox­ylato‐κ2O2,O6)­tetrakis(μ‐pyridine‐3,5‐di­carboxyl­ic acid‐κ2N:O)tetracopper(II): a copper complex with tetrameric molecular units

Crystals of the title tetramer, [Cu₄(C₇H₃NO₄)₄(C₇H₅NO₄)₄(H₂O)₂], were synthesized hydro­thermally at 433 K. The triclinic structure consists of tetrameric molecular species, which interact via strong hydrogen bonds. The Cu^II ions are distributed equally between one square‐pyramidal site and one octahedral site distorted by the Jahn–Teller effect. This coordination complex exhibits the peculiarity of having Cu^II ions linked to both the 2,6‐ and the 3,5‐isomers of pyridine­di­carboxyl­ic acid.     

Spata‐13,17‐diene Synthase—An Enzyme with Sesqui‐, Di‐, and Sesterterpene Synthase Activity from Streptomyces xinghaiensis

A terpene synthase from the marine bacterium Streptomyces xinghaiensis has been characterised, including a full structure elucidation of its products from various substrates and an in‐depth investigation of the enzyme mechanism by isotope labelling experiments, metal cofactor variations, and mutation experiments. The results revealed an interesting dependency of Mn²⁺ catalysis on the presence of Asp‐217, a residue that is occupied by a highly conserved Glu in most other bacterial terpene synthases.     

Tuning the Redox Properties of a Nonheme Iron(III)–Peroxo Complex Binding Redox‐Inactive Zinc Ions by Water Molecules

Redox‐inactive metal ions play important roles in tuning chemical properties of metal–oxygen intermediates. Herein we report the effect of water molecules on the redox properties of a nonheme iron(III)–peroxo complex binding redox‐inactive metal ions. The coordination of two water molecules to a Zn²⁺ ion in (TMC)Fe^III‐(O₂)‐Zn(CF₃SO₃)₂ ( 1 ‐Zn²⁺) decreases the Lewis acidity of the Zn²⁺ ion, resulting in the decrease of the one‐electron oxidation and reduction potentials of 1 ‐Zn²⁺. This further changes the reactivities of 1 ‐Zn²⁺ in oxidation and reduction reactions; no reaction occurred upon addition of an oxidant (e.g., cerium(IV) ammonium nitrate (CAN)) to 1 ‐Zn²⁺, whereas 1 ‐Zn²⁺ coordinating two water molecules, (TMC)Fe^III‐(O₂)‐Zn(CF₃SO₃)₂‐(OH₂)₂ [ 1 ‐Zn²⁺‐(OH₂)₂], releases the O₂ unit in the oxidation reaction. In the reduction reactions, 1 ‐Zn²⁺ was converted to its corresponding iron(IV)–oxo species upon addition of a reductant (e.g., a ferrocene derivative), whereas such a reaction occurred at a much slower rate in the case of 1 ‐Zn²⁺‐(OH₂)₂. The present results provide the first biomimetic example showing that water molecules at the active sites of metalloenzymes may participate in tuning the redox properties of metal–oxygen intermediates.