Studies on taxadiene synthase: interception of the cyclization cascade at the verticillene stage and rearrangement to phomactatriene

The cyclization of geranylgeranyl diphosphate (GGDP) to taxadiene catalyzed by taxadiene synthase has been suggested to proceed in stages, involving a transient bicyclic verticillyl carbocation intermediate, which also has been proposed in the biosynthetic pathway leading to phomactatriene by marine fungi of Phoma sp. On incubation with des-7-methylGGDP, which would be expected to decrease the stability of a carbocation produced by hydride migration, taxadiene synthase produced phomactatrienes as major products. This indicates that the verticillyl carbocation was indeed formed but underwent further skeletal rearrangements, diverging from the usual pathway taken by GGDP en route to taxadiene. Products were identified using GC-MS, one- and two-dimensional NMR, and X-ray crystallography.     

QM/MM study of the taxadiene synthase mechanism

Combined quantum mechanics/molecular mechanics (QM/MM) calculations were used to investigate the reaction mechanism of taxadiene synthase (TXS). TXS catalyzes the cyclization of geranylgeranyl diphosphate (GGPP) to taxadiene (T) and four minor cyclic products. All these products originate from the deprotonation of carbocation intermediates. The reaction profiles for the conversion of GGPP to T as well as to minor products were calculated for different configurations of relevant TXS carbocation complexes. The QM region was treated at the M06-2X/TZVP level, while the CHARMM27 force field was used to describe the MM region. The QM/MM calculations suggest a reaction pathway for the conversion of GGPP to T, which slightly differs from previous proposals regarding the number of reaction steps and the conformation of the carbocations. The QM/MM results also indicate that the formation of minor products via water-assisted deprotonation of the carbocations is highly exothermic, by about −7 to −23 kcal/mol. Curiously, however, the computed barriers and reaction energies indicate that the formation of some of the minor products is more facile than the formation of T. Thus, the present QM/MM calculations provide detailed insights into possible reaction pathways and into the origin of the promiscuity of TXS, but they do not reproduce the product distribution observed experimentally. © 2019 Wiley Periodicals, Inc.     

Novel mechanism for priming aromatic polyketide synthases

In this issue of Chemistry & Biology, a novel priming mechanism is proposed for aromatic polyketide biosynthesis, with an iterative type I polyketide synthase generating a starter unit primed for a type II polyketide synthase. This novel priming system participates in hedamycin biosynthesis, a DNA alkylating agent.     

Antioxidant activity and mechanism of the abietane-type diterpene ferruginol

The antioxidant activity of the abietane-type diterpene ferruginol was evaluated by comparison with that of carnosic acid, ( ± )-α-tocopherol and dibutylhydroxytoluene using 2,2-diphenyl-1-picrylhydrazyl, β-carotene bleaching and linoleic acid assays. Ferruginol had the lowest antioxidant activity of this group using the 2,2-diphenyl-1-picrylhydrazyl and β-carotene methods in polar solvent buffer. However, ferruginol exhibited stronger activity than carnosic acid and α-tocopherol for linoleic acid oxidation under non-solvent conditions. Five peaks corresponding to ferruginol derivatives were detected through GC-MS analysis of the reaction between ferruginol and methyl linoleate. The three reaction products were identified as dehydroferruginol, 7β-hydroxyferruginol and sugiol, and the other two peaks were assumed to be 7α-hydroxyferruginol and the quinone methide derivative of ferruginol. The time course of the reaction suggests that the quinone methide was produced early in the reaction and reacted further to produce dehydroferruginol, 7-hydroxyferruginol and sugiol. Thus, we inferred that quinone methide formation was a key step in the antioxidant reaction of ferruginol.     

Structural control of polyketide formation in plant-specific polyketide synthases

BACKGROUND: Polyketide synthases (PKSs) generate molecular diversity by utilizing different starter molecules and by controlling the final length of the polyketide. Although exploitation of this mechanistic variability has produced novel polyketides, the structural foundation of this versatility is unclear. Plant-specific PKSs are essential for the biosynthesis of anti-microbial phytoalexins, anthocyanin floral pigments, and inducers of Rhizobium nodulation genes. 2-Pyrone synthase (2-PS) and chalcone synthase (CHS) are plant-specific PKSs that share 74% amino acid sequence identity. 2-PS forms the triketide methylpyrone from an acetyl-CoA starter molecule and two malonyl-CoAs. CHS uses a p-coumaroyl-CoA starter molecule and three malonyl-CoAs to produce the tetraketide chalcone. Our goal was to elucidate the molecular basis of starter molecule selectivity and control of polyketide length in this class of PKS.Results: The 2.05 A resolution crystal structure of 2-PS complexed with the reaction intermediate acetoacetyl-CoA was determined by molecular replacement. 2-PS and CHS share a common three-dimensional fold, a set of conserved catalytic residues, and similar CoA binding sites. However, the active site cavity of 2-PS is smaller than the cavity in CHS. Of the 28 residues lining the 2-PS initiation/elongation cavity, four positions vary in CHS. Point mutations at three of these positions in CHS (T197L, G256L, and S338I) altered product formation. Combining these mutations in a CHS triple mutant (T197L/G256L/S338I) yielded an enzyme that was functionally identical to 2-PS.Conclusions: Structural and functional characterization of 2-PS together with generation of a CHS mutant with an initiation/elongation cavity analogous to 2-PS demonstrates that cavity volume influences the choice of starter molecule and controls the final length of the polyketide. These results provide a structural basis for control of polyketide length in other PKSs, and suggest strategies for further increasing the scope of polyketide biosynthetic diversity.     

Proposed mechanism for the reaction catalyzed by a diterpene cyclase,aphidicolan-16beta-ol synthase: experimental results on biomimetic cyclization and examination of the cyclization pathway by ab initio calculations

To examine the mechanism of the cyclization reaction catalyzed by aphidicolan-16beta-ol synthase (ACS), which is a key enzyme in the biosynthesis of diterpene aphidicolin, a specific inhibitor of DNA polymerase alpha, skeletal rearrangement of 2a and biomimetic cyclization of 4b were employed. The structures of the reaction products, which reflect penultimate cation intermediates, allowed us to propose a detailed reaction pathway for the Lewis acid-catalyzed cyclizations and rearrangements. Isolation of these products in an aphidicolin-producing fungus led us to speculate that the mechanism of the ACS-catalyzed cyclization reaction is the same as that of a nonenzymatic reaction. Ab initio calculations of the acid-catalyzed reaction intermediates and the transition states indicate that the overall reaction catalyzed by ACS is an exothermic process though the reaction proceeds via an energetically disfavored secondary cation-like transition state. In conjunction with the solvent effect in the acid-catalyzed reactions, this indicates that the actual role of ACS is to provide a template which enforces conformations of the intermediate cations leading to the productive cyclization although it has been believed that the cation-pi interaction between cation intermediates and aromatic amino acid residues in the active site is important for the enzymatic catalysis. This study provided important information on the role of various cationic species, especially secondary cation-like structures, in both nonenzymatic and enzymatic reactions.     

Intramolecular proton transfer in the cyclization of geranylgeranyl diphosphate to the taxadiene precursor of taxol catalyzed by recombinant taxadiene synthase

BACKGROUND: The committed step in the biosynthesis of the anticancer drug taxol in yew (Taxus) species is the cyclization of geranylgeranyl diphosphate to taxa-4(5),11(12)-diene. The enzyme taxadiene synthase catalyzes this complex olefin cation cyclization cascade involving the formation of three rings and three stereogenic centers. RESULTS: Recombinant taxadiene synthase was incubated with specifically deuterated substrates, and the mechanism of cyclization was probed using MS and NMR analyses of the products to define the crucial hydrogen migration and terminating deprotonation steps. The electrophilic cyclization involves the ionization of the diphosphate with closure of the A-ring, followed by a unique intramolecular transfer of the C11 proton to the re-face of C7 to promote closure of the B/C-ring juncture, and cascade termination by proton elimination from the beta-face of C5. CONCLUSIONS: These findings provide insight into the molecular architecture of the first dedicated step of taxol biosynthesis that creates the taxane carbon skeleton, and they have broad implications for the general mechanistic capability of the large family of terpenoid cyclization enzymes.     

Unprecedented mechanism of chain length determination in fungal aromatic polyketide synthases

Fungal aromatic polyketides show remarkable structural diversity fundamentally derived from variations in chain length and cyclization pattern. Their basic skeletons are synthesized by multifunctional iterative type I polyketide synthases (PKSs). Recently, we have found that the C-terminal thioesterase (TE)-like domain of Aspergillus nidulans WA catalyzes Claisen-type cyclization to form the B-ring of naphthopyrone YWA1. Here we report the unprecedented mechanism of chain length determination by the C-terminal TE-like domain of Colletotrichum lagenarium PKS1, which, in addition to catalyzing Claisen-type cyclization, intercepts the polyketomethylene intermediate from the acyl carrier protein domain during the condensation reaction to produce shorter chain length products. This chain length determination system is novel among PKSs, including bacterial and plant PKSs. The functional diversity of the TE-like domain directly influences the structural diversity of aromatic polyketides in C. lagenarium PKS1.     

Proposed mechanism for the one photon one electron delayed fluorescence in some organic dyes

The one photon delayed fluorescence (DF), the excitation DF, the phosphorescence and the temperature dependence of these emissions in the cosin dye are published and discussed. The same experimental behavior is also observed in a series of dyes in various matrices at 77°K. To explain the primary photo-process, evidences are given in favor of a short-range electron phototransfer in the bulk of clusters formed by the contraction of the liquid solution followed by rigidification of the matrix. The recombination mechanism is also discussed in view of the experimental results.     

Loss of co-linearity by modular polyketide synthases: a mechanism for the evolution of chemical diversity

Modular polyketide synthases biosynthesise natural products through successive Claisen-type condensations, where one module is responsible for one round of chain extension. This review describes recent findings where this rule of co-linearity is broken, either by one module being bypassed (skipping) or through one module being used for multiple chain extension events (stuttering).     

Novel mechanism for the formation of long-chain branching in polyethylene

Polyethylene produced by a vanadium-based polymerization catalyst contains long-chain branching as determined by NMR and rheology, even though the polymer has very low levels of vinyl unsaturation. A new mechanism is proposed for the formation of the long-chain branching, which involves C H bond activation of the polyethylene backbone through a σ-bond metathesis reaction, followed by ethylene insertion at the new V C bond. Consistent with the proposed C H bond activation mechanism, the polymerization catalyst was also found to insert ethylene into the C H bonds of alkanes such as heptane. A bridged metallocene catalyst was also found to activate C H bonds of alkanes suggesting this new mechanism may explain the formation of long-chain branching in some metallocene-produced polyethylene. © 1998 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 36: 2889–2898, 1998     

Stereochemistry of the macrocyclization and elimination steps in taxadiene biosynthesis through deuterium labeling

Taxadiene synthase catalyzes the cyclization of (E,E,E)-geranylgeranyl diphosphate (GGPP) to taxa-4(5),11(12)-diene (Scheme 1, 5 --> 2) as the first committed step of Taxol biosynthesis. Deuterated GGPPs labeled stereospecifically at C-1, C-4, and C-16 were synthesized and incubated with recombinant taxadiene synthase from Taxus brevifolia to elucidate the stereochemistry of the cyclization reaction at these positions. The deuterium-labeled taxadienes obtained from (R)-[1-(2H1)]-, (S)-[1-(2H1)]-, and [16,16,16-(2H3)]GGPPs (9, 10, and 23b) were established to have deuterium in the 2alpha and 2beta CH2 and 16CH3 positions, respectively, by high-field 1H NMR spectroscopy (eqs 1-3). Incubation of (R)-[4-(2H1)]GGPP (17) with the recombinant enzyme gave a 10:10:80 mixture of [5beta-(2H1)]taxa-3(4),11(12)-diene, [5beta-(2H1)]taxa-4(20),11(12)-diene, and unlabeled taxa-4(5),11(12)-diene according to GC/MS analyses of the products (eq 4). It follows that C-1 of GGPP underwent inversion of configuration, that the A ring cyclization occurs on the si face of C15, and that the terminating proton abstraction removes H5beta from the final taxenyl carbocation intermediate. Thus, the C1-C14 and C15-C10 bonds are formed on the opposite faces of the 14,15 double bond of the substrate, i.e., overall anti electrophilic addition. The implications of these findings for the mechanism of the cyclization and rearrangement are discussed.     

A novel reaction mechanism for the formation of deoxyanthocyanidins

The synthesis of deoxyanthocyanidins from the reaction between cinnamic aldehydes (coniferaldehyde and sinapaldehyde) and phloroglucinol is reported herein. The resulting structures were characterized by visible, MS, and NMR spectroscopy.     

Drift mechanism for the formation of metallic wires in liquid helium

A drift mechanism of formation of wires in liquid helium from metal laser ablation products has been suggested. The latter are usually ionized and are attracted to any surface due to the electric image force. This is responsible for that the drift of microparticles prevail over diffusion. The formation of anisometric structures (wires) under the drift conditions is a well-known phenomenon [9], not related to the properties of superfluid helium.     

Reaction mechanism for formation of condensed thienopyrans and thienothiopyrans

The formation of 2-amino-3-cyanothiophenes has been studied. It has been shown that the intermediates in the synthesis are the Knoevenagel type ,-unsaturated nitriles.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 3, pp. 395–397, March, 1987.     

Synthetic models for the zinc sites in the methionine synthases

The syntheses and molecular structures of a series of tetrahedral zinc complexes designed to model the active sites in Escherichia coli methionine synthases are reported. [PhTttBu]ZnBr (PhTttBu = phenyltris((tert-butylthio)-methyl)borate) was prepared and characterized crystallographically to provide entry into [S3]ZnX complexes. Metathesis with KSPh yielded the phenylthiolato complex, [PhTttBu]Zn(SPh), which represents a structural mimic of the homocysteine ligated form of the enzyme. Alternatively, [S2N]ZnX (X = Br, CH3, SPh) species were prepared using the new mixed-donor ligands, [Ph(pz)BttBu] (phenyl(pyrazolyl)bis((tert-butylthio)methyl)borate) and [Ph(pztBu)BttBu] (phenyl(3-tert-butylpyrazolyl)bis((tert- butylthio)methyl)borate). Protonolysis of [Ph(pztBu)-BttBu]Zn(CH3) by PhSH in toluene yielded [Ph(pztBu)BttBu]Zn(SPh), a synthetic analogue of the homocysteine ligated form of cobalamin-independent methionine synthase (Met E). The average Zn-S bond distance in [Ph-(pztBu)BttBu]Zn(SPh) of 2.37 A compares well with the EXAFS-derived distance of 2.31 A found in the homocysteine-bound form of Met E.     

Search for and study of curaremimetic drugs among the diterpene alkaloids

A number of diterpene alkaloids (DAs) and their derivatives have been investigated for curaremimetic activity. Their structure-activity relationships and the mechanisms of their action have been studied. Structural fragments of the DAs that are responsible for curaremimetic properties have been revealed. Among the compounds studied, nudicauline and lycaconitine are superior to the curaremimetic drugs melliktin and condelphine.Institute of the Chemistry of Plant Substances, Academy of Sciences of the Republic of Uzbekistan, Tashkent, fax (3712) 89 14 75. Translated from Khimiya Prirodnykh Soedinenii, No. 6, pp. 841–848, November-December, 1995. Original article submitted April 10, 1995.