Study of IspH, a key enzyme in the methylerythritol phosphate pathway using fluoro-substituted substrate analogues

IspH, a [4Fe-4S]-cluster-containing enzyme, catalyzes the reductive dehydroxylation of 4-hydroxy-3-methyl-butenyl diphosphate (HMBPP) to isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) in the methylerythritol phosphate pathway. Studies of IspH using fluoro-substituted substrate analogues to dissect the contributions of several factors to IspH catalysis, including the coordination of the HMBPP C(4)-OH group to the iron-sulfur cluster, the H-bonding network in the active site, and the electronic properties of the substrates, are reported.     

Mechanistic insights into the reductive dehydroxylation pathway for the biosynthesis of isoprenoids promoted by the IspH enzyme

Here, we report an integrated quantum mechanics/molecular mechanics (QM/MM) study of the bio-organometallic reaction pathway of the 2H⁺/2e^– reduction of (E)-4-hydroxy-3-methylbut-2-enyl pyrophosphate (HMBPP) into the so called universal terpenoid precursors isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP), promoted by the IspH enzyme. Our results support the viability of the bio-organometallic pathway through rotation of the OH group of HMBPP away from the [Fe₄S₄] cluster at the core of the catalytic site, to become engaged in a H-bond with Glu126. This rotation is synchronous with π-coordination of the C2C3 double bond of HMBPP to the apical Fe atom of the [Fe₄S₄] cluster. Dehydroxylation of HMBPP is triggered by a proton transfer from Glu126 to the OH group of HMBPP. The reaction pathway is completed by competitive proton transfer from the terminal phosphate group to the C2 or C4 atom of HMBPP.     

Isoprenoid Biosynthesis in Pathogenic Bacteria: Nuclear Resonance Vibrational Spectroscopy Provides Insight into the Unusual [4Fe‐4S] Cluster of the E. coli LytB/IspH Protein

The LytB/IspH protein catalyzes the last step of the methylerythritol phosphate (MEP) pathway which is used for the biosynthesis of essential terpenoids in most pathogenic bacteria. Therefore, the MEP pathway is a target for the development of new antimicrobial agents as it is essential for microorganisms, yet absent in humans. Substrate‐free LytB has a special [4Fe‐4S]²⁺ cluster with a yet unsolved structure. This motivated us to use synchrotron‐based nuclear resonance vibrational spectroscopy (NRVS) in combination with quantum chemical‐molecular mechanical (QM/MM) calculations to gain more insight into the structure of substrate‐free LytB. The apical iron atom of the [4Fe‐4S]²⁺ is clearly linked to three water molecules. We additionally present NRVS data of LytB bound to its natural substrate, (E)‐4‐hydroxy‐3‐methylbut‐2‐en‐1‐yl diphosphate (HMBPP) and to the inhibitors (E)‐4‐amino‐3‐methylbut‐2‐en‐1‐yl diphosphate and (E)‐4‐mercapto‐3‐methylbut‐2‐en‐1‐yl diphosphate.     

Synthesis of [1-C] and stereo-specifically [1-H] labeled fluorinated substrate analogues of IspH enzyme in the deoxyxylulose phosphate pathway

IspH in the deoxyxylulose phosphate (DXP) pathway catalyzes the reductive dehydration of (E)-4-hydroxy-3-methyl-2-butenyl diphosphate (HMBPP) to isopentenyl diphosphate (IPP) and its isomer dimethylallyl diphosphate (DMAPP), which are the starting materials for the synthesis of thousands of isoprenoids. Several models have been proposed in the literature to account for this unique transformation, and most of them involve the formation of an allylic radical intermediate. To facilitate trapping and characterizing the proposed intermediates in the IspH-catalyzed reactions, in the present work, we report the synthesis of four isotopically labeled IspH substrate analogues. These isotopically labeled mechanistic probes will be utilized in the future for characterizing the proposed IspH reaction intermediates by the combination of bioorganic and biophysical approaches.     

On the Early Steps of Cineol Biosynthesis in Eucalyptus globulus

Samples of [4‐²H₁]‐1‐deoxyxylulose ( 17a ) and [2‐¹³C, 4‐²H₁]‐1‐deoxyxylulose ( 17b ), have been prepared by modification of known procedures and fed in aqueous solution to twiglets of Eucalyptus globulus. The probes of cineol ( 6 ) isolated from these experiments were analyzed by GC/MS, ²H‐ and ¹³C‐NMR techniques. In the experiments with 17b , the formation of five isotopomers of 6 could be detected. Their structure and relative abundance demonstrate that the ¹³C‐label is incorporated to the same extent into the two C₅‐units of 6 , and that the ²H label is retained to an extent of 57% in the starter dimethylallyl‐diphosphate unit (DMAPP; 12 ), but completely or almost completely lost in the unit derived from isopentenyl diphosphate (IPP; 11 ), in the elongation step which leads to geranyl diphosphate (GPP; 1 ). These results confirm that the recently discovered mevalonate‐independent pathway to IPP and DMAPP is operative in the biosynthesis of cineol, and indicate, together with previous finding, that, within this pathway, formation of IPP and DMAPP occurs in independent rather than in sequential steps. In addition, the demonstration of different metabolic origins for the olefinic H‐atoms of GPP ( 1 ), the aliphatic C₁₀‐precursor of 6 , paves the way for a realistic interpretation of the strikingly consistent but hitherto unexplained anomalies detected in the natural‐abundance ²H‐NMR spectra of (+)‐ and (−)‐α‐pinene and of (+)‐limonene.     

IspH protein of Escherichia coli: studies on iron-sulfur cluster implementation and catalysis

The ispH gene of Escherichia coli specifies an enzyme catalyzing the conversion of 1-hydroxy-2-methyl-2-(E)-butenyl diphosphate into a mixture of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) in the nonmevalonate isoprenoid biosynthesis pathway. The implementation of a gene cassette directing the overexpression of the isc operon involved in the assembly of iron-sulfur clusters into an Escherichia coli strain engineered for ispH gene expression increased the catalytic activity of IspH protein anaerobically purified from this strain by a factor of at least 200. For maximum catalytic activity, flavodoxin and flavodoxin reductase were required in molar concentrations of 40 and 12 microM, respectively. EPR experiments as well as optical absorbance indicate the presence of a [3Fe-4S](+) cluster in IspH protein. Among 4 cysteines in total, the 36 kDa protein carries 3 absolutely conserved cysteine residues at the amino acid positions 12, 96, and 197. Replacement of any of the conserved cysteine residues reduced the catalytic activity by a factor of more than 70 000.     

Chiral [2H]-Labelled Methylene Groups in Trienoic- and Dienoic Fatty Acids: A Facile Approach via Asymmetric Epoxidation of [2H] Allyl Alcohols

Chiral [²H] -labelled methylene groups flanked by two double bonds within (poly)unsaturated fatty acids are readily available from trans-2,3-epoxy[2,3-²H₂] alk-4-yn-l-ols, obtained in their turn by asymmetric epoxidation of the corresponding (E)-[2,3-²H₂] alk-2-en-4-yn-l-ols (see Scheme 3). The procedure is exemplified for (8S,3Z,6Z,9Z)-[7,8-²H₂] trideca-3,6,9-trienoic acid ((8S)- 11 ) and (8R)- 11 (Scheme 4) as well as for (5S,3Z,6Z)-[4,5^?2H₂]deca-3,6-dienoic acid ((5S)- 13 ) and (5R)- 13 (Scheme 5).     

Organoruthenaborane Chemistry. X. The SM2-catalysed formation of [ l-(η6-C6Me6)-isocloso-RuB9H9], and some B-phenylamino derivatives. NMR and X-ray diffraction studies

The action of SMe₂ on the ten-vertex nido-ruthenaborane [6-(η⁶-C₆Me₆)RuB₉H_l3] ( 1 ) provides a high-yield route to the unsubstituted isocloso-ruthenaborane [1-(η⁶-C₆Me₆)RuB₉H₉] (2). The benzene analogue [1-(η⁶-C₆Me₆)RuB₉H₉] is prepared similarly. By contrast, reaction of (1) with PhNH₂ gives a variety of B-phenylamino isocloso derivatives, including orange crystals of [1-(η⁶-C₆Me₆)-2-(PhNH)-isocloso-1-RuB 9 H₈] ( 3 ), red-orange [1-(η⁶-C₆Me₆)-2,3-(PhNH)₂-isocloso-1-RuB₉H₇] ( 4 ) and dark-red [1-(η⁶-C₆Me₆)-5,6,7-(PhNH)₃-isocloso-1-RuB₉H₆] ( 5 ). Detailed ¹H and ¹¹B nmr properties of these various compounds are described. The structure of ( 3 ) has been established by a single-crystal X-ray diffraction study of the solvate [1-(η⁶-C₆Me₆)-2-(PhNH)-isocloso-1-RuB₉H₈] · 1/2 CH₂Cl₂; the crystals were monoclinic, space group C2/c, with a = 1895.1(3), b = 1556.6(3), c = 1716.4(3) pm, β = 104.37(1)° and z = 8.     

Reaction of ketenes with N,N-disubstituted α-aminomethyleneketones. XIII. Synthesis of 2H-pyrano[3,2-d]-1-benzoxepin derivatives

Cycloaddition of dichloroketone to N,N-disubstituted (E)-4-aminomethylene-3,4-dihydro-1-benzoxepin-5(2H)-ones gave N,N-disubstituted 4-amino-3,3-dichloro-3,4,5,6-tetrahydro-2H-pyrano[3,2-d]-1-benzoxepin-2-ones II, which are derivatives of the new heterocyclic system 2H-pyrano[3,2-d]-1-benzoxepin. Dehydrochlorination with triethylamine of II afforded N,N-disubstituted 4-amino-3-chloro-5,6-dihydro-2H-pyrano-[3,2-d]-1-benzoxepin-2-ones III in good to moderate yields. In the triethylamine treatment of IIh (NR₂ = diphenylamino), 3-chloro-5,6-dihydro-2H-pyrano[3,2-d]-1-benzoxepin-2-one was isolated in low yield near to IIIh, whereas IIc (NR² = diisopropylamino) gave in low yield 4-diisopropylamino-5,6-dihydro-2H-pyrano(3,2-d)-1-benzoxepin-2-one.     

Synthesis and Circular Dichroism of Both Enantiomers of 2-deuterofluoroacetic acid ( Fluoro[2H1]acetic acid)

Sharpless epoxidation of (E)-1-(trimethylsilyl)[1-²H₁]oct-1-en-3-o1 ( 3a ) yielded (1S,2S,3S)- and (1R,2R,3R)-1-(trimethylsilyl)-1,2-epoxy[1-²H₁]octan-3-ols ( 4a and 4b , resp.) which were converted in three steps into (S)- and (R)-fluoro[ ²H₁]acetic acid ( 7a and 7b , resp.) in good yields. Their high isotopic and optical purity was established by ¹H- and ¹⁹F-NMR, mass, and circular-dichroism spectroscopy.     

The Allylic Oxidation of Geraniol Catalyzed by Cytochrome P-450Cath., Proceeding with retention of configuration

Incubation of the geraniols (R)-(8-²H₁)[8-³H₁]- 1 and (S)-(8-²H₁)[8-³H₁]- 1 with microsomal cytochrome P-450_Cath. from the subtropical plant Catharanthus roseus (L.)G. DON resulted in the formation of the chiral 8-hydroxygeraniols (S)-(8-²H₁)[8-³H₁]- 2 and (R)-(8-²H₁)[8-³H₁]- 2 . Their absolute configuration was assigned on the basis of the ¹H-decoupled ³H-NMR Spectra of the corresponding dicamphanates (S)-(8-²H₁)[8-³H₁]- 9 and (R)-(8-²H₁)[8-³H₁]- 9 , of which the configurations are established in relation to the synthetic reference samples. The results clearly indicate retention of configuration during the allylic oxidation of 1 .     

Singlet-Oxygen Ene Reactions of (E)-4-Propyl[1,1,-2H3]oct-4-ene. Short Communication

Rose bengal-sensitized photooxygenation of 4-propyl-4-octene ( 1 ) in MeOH/Me₂CHOH 1:1 (v/v) and MeOH/H₂O 95:5 followed by reduction gave (E)-4-propyl-5-octen-4-ol ( 4 ), its (Z)-isomer 5 , (E)-5-propyl-5-octen-4-ol ( 6 ), and its (Z)-isomer 7 . Analogously, (E)-4-propyl[1,1,1-²H₃]oct-4-ene ( 2 ) gave (E)-4-propyl[1,1,1-²H₃]oct-5-en-4-ol ( 14 ), its (Z)-isomer 15 , (E)-5-[3′,3′,3′-²H₃]propyl-5-octen-4-ol ( 16 ), its (Z)-isomer 17 , and the corresponding [8,8,8-²H₃]-isomers 18 and 19 (see Scheme 1). The proportions of 4–7 were carefully determined by GC between 10% and 85% conversion of 1 and were constant within this range. The labeled substrate 2 was photooxygenated in two high-conversion experiments, and after reduction, the ratios 16/18 and 17/19 were determined by NMR. Isotope effects in 2 were neglected and the proportions of corresponding products from 1 and 2 assumed to be similar (% 4 ≈? % 14 ; % 5 ≈? % 15 ; % 6 ≈? % ( 16 + 18 ): % 7 ≈? % ( 17 + 19 )). Combination of these proportions with the ratios 16/18 and 17/19 led to an estimate of the proportions of hydroperoxides formed from 2 . Accordingly, singlet oxygen ene additions at the disubstituted side of 2 are preferred (ca. 90%). The previously studied trisubstituted olefins 20–25 exhibited the same preference, but had both CH₃ and higher alkyl substituents on the double bond. In these substrates, CH₃ groups syn to the lone alkyl or CH₃ group appear to be more reactive than CH₂ groups at that site beyond a statistical bias.     

Synthese von diastereo- und enantio-selektiv deuterierten β,ε-, β,β-, β,γ- und γ,γ-Carotinen

Synthesis of Diastereo- and Enantioselectively Deuterated β,ε-, β,β-, β,γ- and γ,γ-Carotenes We describe the synthesis of (1′R, 6′S)-[16′, 16′, 16′-²H₃]-β, εcarotene, (1R, 1′R)-[16, 16, 16, 16′, 16′, 16′-²H₆]-β, β-carotene, (1′R, 6′S)-[16′, 16′, 16′-²H₃]-γ, γ-carotene and (1R, 1′R, 6S, 6′S)-[16, 16, 16, 16′, 16′, 16′-²H₆]-γ, γ-carotene by a multistep degradation of (4R, 5S, 10S)-[18, 18, 18-²H₃]-didehydroabietane to optically active deuterated β-, ε- and γ-C₁₁-endgroups and subsequent building up according to schemes \documentclass{article}\pagestyle{empty}\begin{document}${\rm C}_{11} \to {\rm C}_{14}^{C_{\mathop {26}\limits_ \to }} \to {\rm C}_{40} $\end{document} and C₁₁ → C₁₄; C₁₄+C₁₂+C₁₄→C₄₀. NMR.- and chiroptical data allow the identification of the geminal methyl groups in all these compounds. The optical activity of all-(E)-[²H₆]-β,β-carotene, which is solely due to the isotopically different substituent not directly attached to the chiral centres, is demonstrated by a significant CD.-effect at low temperature. Therefore, if an enzymatic cyclization of [17, 17, 17, 17′, 17′, 17′-²H₆]lycopine can be achieved, the steric course of the cyclization step would be derivable from NMR.- and CD.-spectra with very small samples of the isolated cyclic carotenes. A general scheme for the possible course of the cyclization steps is presented.     

Synthesis of 1-Methyl- and 1-Phenyl-closo-B12H121- by Cross Coupling of 1-Iodo-closo-B12H121- with Methyl- and Phenylzinc Chlorides,Catalyzed by Palladium Complexes

Reactions of [N⁺(n-C₄H₉)₄]₂[1-I-closo-B_{1 2}H₁ ² ₁ ^-] with MeZnCl and PhZnCl, catalyzed by (Ph₃P)₄Pd, in THF solution gave, respectively, [N⁺(n-C₄H₉)₄]₂[1-CH₃-closo-B_{1 2}H₁ ² ₁ ^-] and [N⁺(n-C₄H₉)₄]₂ [1-Ph-closo-B_{1 2}H₁ ² ₁ ^-] in good yields.     

N-arylammonio- and N-pyridinium-substituted derivatives of dodecahydro-closo-dodecaborate(2-)

We report two methods for preparing N-arylammonio, N-pyridyl and N-arylamino dodecaborates: heating of the tetrabutylammonium salt of dodecahydro-closo-dodecaborate(2-) with aryl and pyridyl amines, or nucleophilic attack of [closo-B₁₂H₁₁NH₂]²⁻ on a strongly deactivated aromatic system. With aryl amines we obtained [1-closo-B₁₂H₁₁N(R¹)₂C₆H₅]⁻ (R¹ = H, CH₃). With 4-(dimethylamino)pyridine, [1-closo-(B₁₂H₁₁NC₅H₄)-4-N(CH₃)₂]⁻, with a bond between the boron and the pyridinium nitrogen, was obtained. A presumable mechanism for this kind of reactions is reported. By nucleophilic substitution, two products, [1-closo-(B₁₂H₁₁NHC₆H₃)-3,4-(CN)₂]²⁻ and [1-closo-(B₁₂H₁₁NHC₆H₂)-2-(NO₂)-4,5-(CN)₂]²⁻, were formed with 4-nitrophthalonitrile and 1-chloro-2,4-dinitrobenzene gave [1-closo-(B₁₂H₁₁NHC₆H₃)-2,4-(NO₂)₂]²⁻. For [1-closo-B₁₂H₁₁N(CH₃)₂C₆H₅]⁻ and [1-closo-(B₁₂H₁₁NHC₆H₃)-2,4-(NO₂)₂]²⁻ single crystal X-ray structures were obtained.     

Synthesis of deuterium-labelled substrates for the study of oleuropein biosynthesis in Olea europaea callus cultures

We propose the cell culture approach to investigate oleuropein (1) biogenesis in Olea europaea L. We suggest employing olive callus cultures to identify the iridoidic precursor of oleuropein. In fact, we confirmed that callus cells from olive shoot explants are able to produce key secoiridoid as 1. To enable this approach, we synthesised and characterised deuterium-labelled iridoidic precursors belonging both to the loganin and the 8-epiloganin series. These iridoids are [7,8-²H₂]-7-deoxy-8-epi-loganin (2^D), [8,10-²H₂]-8-epi-loganin (4^D) and [7,8-²H₂]-7-deoxy-loganin (3^D).     

Synthesis of some novel 5-substituted benzamido-6-arylamino-pyrazolo[3,4-D]pyrimidin-4-one derivatives for herbicidal activity

Abstract

Sixteen novel 3-methylthio-5-substituted benzamido-6-arylamino-1-phenyl-1H-pyrazolo[3,4-d]pyrimidin-4 (5H)-one derivatives (4a–p) were successfully synthesized from iminophosphoranes, aryl isocyanate, and substituted benzoylhydrazine. The structures of the title compounds were elucidated by FT-IR, ¹H NMR, ¹³C NMR, and HRMS. Herbicidal activity of the compounds 4a–p against Brassica napus (rape), Echinochloa crusgalli (barnyard grass), Cucumis sativus (cucumber), and Triticum aestivum (wheat) were determined. The results showed that 5-(2-chlorobenzamido)-6-phenylamino-3-methylthio-1-phenyl-1H-pyrazolo[3,4-d]pyrimidin-4 (5H)-one (4c) displayed remarkable inhibition activity against the stalk and root of rape with 100% inhibition rate at the dosages of 10?mg/L and 100?mg/L, and 5-(4-nitrobenzamido)-6-phenylamino-3-methylthio-1-phenyl-1H-pyrazolo[3,4-d]pyrimidin-4 (5H) -one (4d) exhibited excellent activity against the stalk and root of barnyard grass with 100% inhibition rate at the same dosages.     

A new one‐dimensional cadmium(II) coordination polymer incorporating 4‐[4‐(1H‐imidazol‐1‐yl)phenyl]pyridine and 5‐hydroxybenzene‐1,3‐dicarboxylate ligands

The design and synthesis of new organic lgands is important to the rapid development of coordination polymers (CPs). However, CPs based on asymmetric ligands are still rare, mainly because such ligands are usually expensive and more difficult to synthesize. The new asymmetric ligand 4‐[4‐(1H‐imidazol‐1‐yl)phenyl]pyridine (IPP) has been used to construct the title one‐dimensional coordination polymer, catena‐poly[[[aqua{4‐[4‐(1H‐imidazol‐1‐yl‐κN³)phenyl]pyridine}cadmium(II)]‐μ‐5‐hydroxybenzene‐1,3‐dicarboxylato‐κ³O¹,O^1′:O³] monohydrate], {[Cd(C₈H₄O₅)(C₁₄H₁₁N₃)₂(H₂O)]·H₂O}_n, under hydrothermal reaction of IPP with Cd^II in the presence of 5‐hydroxyisophthalic acid (5‐OH‐H₂bdc). The Cd^II cation is coordinated by two N atoms from two distinct IPP ligands, three carboxylate O atoms from two different 5‐OH‐bdc²⁻ dianionic ligands and one water O atom in a distorted octahedral geometry. The cationic [Cd(IPP)₂]²⁺ nodes are linked by 5‐OH‐bdc²⁻ ligands to generate a one‐dimensional chain. These chains are extended into a two‐dimensional layer structure via O—H…O and O—H…N hydrogen bonds and π–π interactions.     

Synthesis and spectroscopic characterization of palladium(II) complexes with 6,8-dimethylimidazo[1,5- a ]-1,3,5-triazin-4( 3H )-one and 6,8-dimethyl-2-thioxo-2,3-dihydroimidazo-[1,5- a ]-1,3,5-triazin-4( 1H )-one

The preparation and spectroscopic study (¹H, ¹³C, ¹⁵NNMR, ¹³CP MAS NMR, IR) of new Pd^II complexes with 6,8-dimethylimidazo[1,5-a]-1,3,5-triazin-4(3H)-one (6,8-DiMe-4-O-IMT) (1) and 6,8-dimethyl-2-thioxo-2,3-dihydroimidazo[1,5-a]-1,3,5-triazin-4(1H)-one (6,8-DiMe-4-O-2-S-IMT) (2) is reported. The spectroscopic data indicate a square planar geometry with two N(7) bonded heterocycles and two cis-chloride anions. The final product of the thermal decomposition of cis-PdCl₂(6,8-DiMe-4-O-IMT)₂ (3) is metallic Pd, whereas for cis-PdCl₂(6,8-DiMe-4-O-2-S-IMT)₂ (4) it is metallic Pd plus C.     

One-pot synthesis of chromeno[2,3-b]isoindolo[1,2-e]pyrrole-12,13-dione derivatives by sequential reaction of ninhydrin, 2-aminochromen-4-ones and arylamines

Stirring an equimolar mixture of ninhydrin 1 and 2-aminochromen-4-ones 2 in CH₃COOH at room temperature produced 6a,11a-dihydroxy-6H-chromeno[2,3-b]indeno[2,1-d]pyrrole-11,12(6aH,11aH)-diones 3, which on heating with aromatic amines 6 in acetic acid produced 11b-hydroxy-7-N-arylimino-6H-chromeno[2,3-b]isoindolo[1,2-e]pyrrole-12,13(11bH)-diones 7.