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Bifunctional abietadiene synthase: mutual structural dependence of the active sites for protonation-initiated and ionization-initiated cyclizations.

Abietadiene synthase from grand fir catalyzes two sequential, mechanistically distinct cyclizations, of geranylgeranyl diphosphate and of copalyl diphosphate, in the formation of a mixture of abietadiene isomers as the committed step of diterpenoid resin acid biosynthesis. Each reaction is independently conducted at a separate active site residing in what were considered to be structurally distinct domains typical of terpene cyclases. Despite the presence of an unusual 250-residue N-terminal insertional element, a tandem pair of charged residues distal to the insertion was shown to form a functional part of the C-terminal active site. Because abietadiene synthase resembles the ancestral plant terpene cyclase, this observation suggests an early evolutionary origin of catalytically important positively charged residues at the N-terminus of enzymes of this general class. A series of N- and C-terminal truncations of this enzyme were constructed and characterized, both alone and as mixtures of adjacent polypeptide pairs, to assess the proposed domain architecture, the function of the insertional element, and the role of presumptive interdomain contacts. These studies indicated a requirement for the insertional element in functional folding and allowed definition of the minimum primary structure of N- and C-terminal active site peptides. Most importantly, the results showed that, although the two active sites of abietadiene synthase are catalytically independent, substantial contact between the two regions is essential for the functional competence of this enzyme. Thus, the two cyclization sites of abietadiene synthase cannot be dissected into catalytically distinct domains, and, therefore, abietadiene synthase is unlikely to have arisen by fusion of two previously independent genes.

Abies↗

Mutational analysis of posttranslational heterocycle biosynthesis in the gyrase inhibitor microcin B17: distance dependence from propeptide and tolerance for substitution in a GSCG cyclizable sequence.

Microcin B17 (MccB17) is a peptidyl antibiotic that is secreted in stationary phase by several strains of Escherichia coli. The antibiotic efficacy of this polypeptide depends on the posttranslational modification of eight cysteine and serine residues to thiazoles and oxazoles, respectively, within the 69 aa McbA structural gene product. Mono- and bisheterocycle formation is mediated by MccB17 synthetase, an enzyme complex composed of three proteins: McbB, -C, and -D. After substrate processing, an N-terminal 26 aa propeptide sequence is cleaved to afford the mature antibiotic. A method for the overexpression and rapid purification of microcin synthetase has been developed using a calmodulin-binding peptide tag. The determinants of substrate recognition and synthetase-mediated heterocycle formation were investigated by a systematic evaluation of 15 McbA1-46 analogues representing minimal substrates containing the first bisheterocyclization site (Gly39-Ser40-Cys41-Gly42) and variants thereof. Each substrate analogue was overexpressed and affinity-purified as fusions to maltose-binding protein, incubated with purified synthetase, and evaluated for processing by Western blots, UV spectroscopy, and mass spectrometry. Insights gained into the process of enzymatic heterocycle formation from cysteine and serine residues are discussed, including the distance dependence of the first cyclized residue from the propeptide and the local sequence context at the cyclizable sites. A model for McbA substrate recognition and processing by MccB17 synthetase is proposed.

ATP-Binding Cassette Transporters↗

The reaction mechanism for CD38. A single intermediate is responsible for cyclization, hydrolysis, and base-exchange chemistries.

Human recombinant CD38 catalyzes the formation of both cyclic ADP-ribose and ADP-ribose products from NAD+ and hydrolyzes cyclic ADP-ribose to ADP-ribose. The corresponding GDP products are formed from NGD+. The enzyme was characterized by substrate and inhibition kinetics, exchange studies, rapid-quench reactions, and stopped-flow-fluorescence spectroscopy to establish the reaction mechanism and energetics for individual steps. Noncyclizable substrates NMN+ and nicotinamide-7-deaza-hypoxanthine dinucleotide (7-deaza NHD+) were rapidly hydrolyzed by the enzyme. The kcat for NMN+ was 5-fold higher than that of NAD+ and has the greatest reported kcat of any substrate for CD38. 7-deaza-NHD+ was hydrolyzed at approximately one-third the rate of NHD+ but does not form a cyclic product. These results establish that a cyclic intermediate is not required for substrate hydrolysis. The ratio of methanolysis to hydrolysis for cADPR and NAD+ catalyzed by CD38 increases linearly with MeOH concentration. Both reactions produce predominantly the beta-methoxy riboside compound, with a relative nucleophilicity of MeOH to H2O of 11. These results indicate the existence of a stabilized cationic intermediate for all observed chemistries in the active site of CD38. The partitioning of this intermediate between cyclization, hydrolysis, and nicotinamide-exchange unites the mechanisms of CD38 chemistries. Steady-state and pre-steady-state parameters for the partition and exchange mechanisms allowed full characterization of the reaction coordinate. Stopped-flow methods indicate a burst of cGDPR formation followed by the steady-state reaction rate. A lag phase, which was NGD+ concentration dependent, was also observed. The burst size indicates that the dimeric enzyme has a single catalytic site formed by two subunits. Pre-steady-state quench experiments did not detect covalent intermediates. Nicotinamide hydrolysis of NGD+ precedes cyclization and the chemical quench decomposes the enzyme-bound species to a mixture of cyclic and hydrolysis products. The time dependence of this ratio indicated that nicotinamide bond-breakage occurs 4 times faster than the conversion of the intermediate to products. Product release is the overall rate-limiting step for enzyme reaction with NGD+.

ADP-ribosyl Cyclase↗

The magnesium-ene cyclization stereochemically directed by an allylic oxyanionic group and its application to a highly stereoselective synthesis of (+/-)-matatabiether. Allylmagnesium compounds by reductive magnesiation of allyl phenyl sulfides.

The first example of a magnesium-ene cyclization stereochemically directed by an allylic oxyanionic group is demonstrated by a highly stereoselective synthesis of the bicyclic terpene matatabiether 10. The synthetic method is particularly valuable, not only because of the stereochemical control and the utility of the versatile hydroxyl group introduced into the product, but also because the precursor of the allylmagnesium is an allyl phenyl sulfide, which is more stable and more easily prepared in a connective fashion than the usual allyl halide precursor. Since the presence of lithium ions encourages undesirable proton transfer to the cyclized organometallic and is detrimental to the stereochemical control, the conversion of the allylic thioether to the allylmagnesium utilizes a lithium-free method involving direct reductive magnesiation in the presence of the magnesium-anthracene complex.

Journal Article↗

The importance of the ene reaction for the C(2)-C(6) cyclization of enyne-allenes.

The present study establishes the ene reaction as a competing reaction mechanism to the diradical mechanism for the thermal C(2)-C(6) cyclization of enyne-allenes which possess bulky substituents at the alkyne terminus. Both reaction routes are found to possess nearly equal free energies of activation. As shown by our computations, primary H/D isotope effects could be used for a definite decision about the mechanism. Concerning the regioselectivity of the cyclization reactions of enyne-allenes our study resolves a long-standing deviation between theoretical results and experimental findings.

Journal Article↗

Preparation of new catalysts by the immobilization of palladium(II) species onto silica: an investigation of their catalytic activity for the cyclization of aminoalkynes.

Silica-immobilized palladium catalysts are readily prepared by treating partially dehydroxylated silica with solutions of the palladium(II) complexes, cis-[PdMeXL2] (X = Me, L2 = dmpe; X = Cl, L2 = dmpe, dppe, phen, bipy, 2PMe3), trans-[PdMeXL2] (X = Cl, NO3, OTf, L = PMe3; X = Cl, L = PPh3), or [PdPh(OH)L]2 (L = PPh3, PCy3), at room temperature. A chemisorption reaction is presumed to occur on the surface Si-OH groups, with elimination of 1 equiv of methane, benzene, or water and the initial formation of a covalent Pd-O bond to the silica surface. The amount of chemisorbed material is strongly dependent on the nature of the complex employed, and the Pd content of the materials, determined by ICP analysis, was found to vary widely (from 1.47 to 0.021 wt %). It appears that the complexes stabilized by more basic ligands undergo a more facile reaction with the surface. The catalytic activity of the materials was first tested in the cyclization of 6-aminohex-1-yne. Higher conversions were found for those catalysts containing more basic ligands, due to the higher loadings, and for those complexes containing more weakly coordinating anions. Silica/trans-[PdMe(NO3)(PMe3)2] was identified as the best catalyst and was used to test the generality of the catalytic cyclization method with two other alkynes, namely, 5-phenyl-4-pentyn-1-amine and 6-phenyl-5-hexyn-1-amine. The catalysts prepared here show rates comparable to, or greater than, those found for homogeneous late transition metal complexes, including their molecular precursors. Furthermore, the supported catalysts are only slightly air-sensitive and can be recycled, after filtration in air, with only moderate loss of activity.

Journal Article↗

The effect of backbone cyclization on the thermodynamics of beta-sheet unfolding: stability optimization of the PIN WW domain.

Backbone cyclization is often used in attempts to enhance protein stability, but is not always successful as it is possible to remove stabilizing or introduce destabilizing interactions in the process. Cyclization of the PIN1 WW domain, a 34-residue three-stranded beta-sheet structure, removes a favorable electrostatic interaction between its termini. Nevertheless, optimization of the linker connecting the N- and C-termini using information based on the previously determined ensemble of NMR structures leads to beta-sheets that are more stable than those derived from the linear sequence. Linkers that are too short or too long introduce strain, likely disrupting native interactions, leading to cyclic folds that are less stable than that of the linear sequence.

Amino Acid Sequence↗

7-N-(mercaptoalkyl)mitomycins: implications of cyclization for drug function.

The Kyowa Hakko Kogyo and Bristol-Myers Squibb companies reported that select mitomycin C(7) aminoethylene disulfides displayed improved pharmacological profiles compared with mitomycin C (1). Mechanisms have been advanced for these mitomycins that differ from 1. Central to many of these hypotheses is the intermediate generation of 7-N-(2-mercaptoethyl)mitomycin C (5). Thiol 5 has been neither isolated nor characterized. Two efficient methods were developed for mitomycin (porfiromycin) C(7)-substituted thiols. In the first method, the thiol was produced by a thiol-mediated disulfide exchange process using an activated mixed mitomycin disulfide. In the second route, the thiol was generated by base-mediated cleavage of a porfiromycin C(7)-substituted thiol ester. We selected four thiols, 7-N-(2-mercaptoethyl)mitomycin C (5), 7-N-(2-mercaptoethyl)porfiromycin (12), 7-N-(2-mercapto-2-methylpropyl)mitomycin C (13), and 7-N-(3-mercaptopropyl)porfiromycin (14), for study. Thiols 5 and 12-14 differed in the composition of the alkyl linker that bridged the thiol with the mitomycin (porfiromycin) C(7) amino substituent. Thiol generation was documented by HPLC and spectroscopic studies and by thiol-trapping experiments. The linker affected the structure of the thiol species and the stability of the thiol. We observed that thiols 5 and 12 existed largely as their cyclic isomers. Evidence is presented that cyclization predominantly occurred at the mitomycin C(7) position. Correspondingly, alkyl linker substitution (13) or extension of the linker to three carbons (14) led to enhanced thiol stability and the predominant formation of the free thiol species. The dominant reaction of thiols 5 and 12-14 or their isomers was dimerization, and we found no evidence that thiol formation led to mitosene production and aziridine ring-opening. These findings indicated that thiol generation was not sufficient for mitomycin ring activation. The potential pharmacological advantages of mitomycin C(7) aminoethylene disulfides compared with 1 is discussed in light of the observed thiol cyclization pathway.

Animals↗

Self-terminating, oxidative radical cyclizations: a novel reaction of acyloxyl radicals.

Acyloxyl radicals RC(O)O* (with R = alkyl, aryl) could be trapped through addition to cyclic and open-chain alkynes, where they were found to act as a donor of oxygen atoms. Mechanistically, this radical oxygenation proceeded through a transannular or intramolecular, respectively, radical cyclization cascade, which was finally terminated by release of an acyl radical RC*(O). The reaction led to stereoselective formation of cyclized products, which contained a carbonyl group at the former site of the alkyne triple bond.

Journal Article↗

Anionic cyclization of a cross-conjugated enediyne.

Cross-conjugated enediynes cannot follow the Bergman cycloaromatization as it involves a methylenediyne moiety with only five pi e(-), insufficient for aromatization. Under reductive conditions the cyclization is made feasible by generating a product with a Hückel number of pi electrons. We illustrate this principle and demonstrate for the first time an anionic cyclization of a cross-conjugated enediyne that results in formation of a five-membered ring. 9-(3-Phenyl-1-phenylethynylprop-2-ynylidene)-9H-fluorene (3) was reduced by potassium to yield the dianion of 9-(3,4-diphenylcyclopenta-2,4-dienylidene)-9H-fluorene (4(2-)), which contains a cyclopentadienyl fragment, and oxidation with iodine yielded the unstable fulvalene 4.

Alkynes↗

C1-c5 photochemical cyclization of enediynes.

This study reports a new photochemical cyclization of tetrafluoropyridinyl (TFP)-substituted enediynes that is accompanied with four formal hydrogen-atom abstractions from organic substrates and is mechanistically different from the Bergman cyclization.

Journal Article↗

A short synthetic route to (+)-austamide, (+)-deoxyisoaustamide, and (+)-hydratoaustamide from a common precursor by a novel palladium-mediated indole --> dihydroindoloazocine cyclization.

The first synthesis of (+)-austamide (1), (+)-deoxyisoaustamide (2), and (+)-hydratoaustamide (10) by a very direct route is described (Scheme 1). Starting from tryptophan methyl ester (3) intermediate 5 is generated in two steps in >98% overall yield. The key step in the synthesis is a novel cyclization of 5 involving organopalladium intermediates which gives the dihydroazocine 6. From this key intermediate the target structures are accessible in just a few steps as shown in Scheme 1. The remarkable conversion of 5 --> 6 can be rationalized by the mechanistic pathway shown in Scheme 2 that involves a multistep sequence which includes palladation, cyclization, and rearrangement.

Azocines↗

Anodic cyclization reactions: capitalizing on an intramolecular electron transfer to trigger the synthesis of a key tetrahydropyran building block.

An anodic cyclization reaction between an enol ether radical cation and an oxygen nucleophile has been used to make a tetrahydropyran building block for the C(10)-C(16) portion of bryostatin. The oxidative cyclization was successful despite the presence of a thioacetal group that has a lower oxidation potential than the enol ether. Experimental evidence suggested that the reaction proceeded through an initial oxidation of the thioacetal followed by an intramolecular electron transfer to form the enol ether radical cation that was subsequently trapped by the oxygen nucleophile. The formation of the desired cyclic product could be explained using the Curtin-Hammett principle. By taking advantage of the intramolecular electron-transfer reaction, we used the presence of a thioacetal in an electrolysis substrate to selectively oxidize a proximal enol ether in the presence of an otherwise identical but more remote enol ether.

Electrodes↗

Microcin J25 has a threaded sidechain-to-backbone ring structure and not a head-to-tail cyclized backbone.

Microcin J25 is a 21 amino acid bacterial peptide that has potent antibacterial activity against Gram-negative bacteria, resulting from its interaction with RNA polymerase. The peptide was previously proposed to have a head-to-tail cyclized peptide backbone and a tight globular structure (Blond, A., Péduzzi, J., Goulard, C., Chiuchiolo, M. J., Barthélémy, M., Prigent, Y., Salomón, R. A., Farías, R. N., Moreno, F. & Rebuffat, S. Eur. J. Biochem. 1999, 259, 747-755). It exhibits remarkable thermal stability for a peptide of its size lacking disulfide bonds and in part this was previously proposed to derive from its macrocyclic structure. We show here that in fact the peptide does not have a head-to-tail cyclic structure but rather a side chain to backbone cyclization between Glu8 and the N-terminus. This creates an embedded ring that is threaded by the C-terminal tail of the molecule, forming a noose-like feature. The three-dimensional structure deduced from NMR data suggests that slippage of the noose is prevented by two aromatic residues flanking the embedded ring. Unthreading does not occur even when the molecule is enzymatically digested with thermolysin. The new structural interpretation fully accounts for previously reported NMR and biophysical data and is consistent with the remarkable stability of this potent antimicrobial peptide.

Amino Acid Sequence↗

Cascade cyclizations and couplings involving nickel enolates.

A new strategy for effecting cascade cyclization processes using nickel enolates has been developed. Nickel enolates may be cleanly generated by the oxidative cyclization of an enal and alkyne with Ni(0), and the resulting enolate may be functionalized by a variety of alkylation processes. Partially and fully intramolecular versions of the process allow the rapid synthesis of complex polycyclics from simple achiral, acyclic precursors.

Journal Article↗

Bis-silicon-bridged stilbene homologues synthesized by new intramolecular reductive double cyclization.

A homologous series of bis-silicon-bridged stilbenes has been synthesized on the basis of a new intramolecular reductive cyclization of bis(o-silyl)-diphenylacetylene. Thus, the reaction of bis(o-silyl)-diphenylacetylenes with excess lithium naphthalenide undergoes the two-electron reduction at the acetylene moiety to produce a dianion intermediate, which further undergoes a double cyclization in a 5-exo mode to produce the bis-silicon-bridged stilbenes. This methodology can also be applied to the synthesis of tetrakis-silicon-bridged bis(styryl)benzenes. The silicon-bridged pi-conjugated systems thus prepared show intense fluorescence in the visible region. Comparison of a bis-silicon-bridged stilbene with its carbon analogue demonstrates the substantial effects of the silicon-bridges on the electronic structures and thus on the fluorescence properties.

Journal Article↗

Deuterium-labeling and NMR study of the dearomatization of N-alkyl-N-benzyldiphenylphosphinamides through anionic cyclization: ortho and benzylic lithiation directed by complex-induced proximity effects.

The mechanism of the anionic cyclization dearomatizing reaction of N-benzyl-N-methyldiphenylphosphinamide (1) upon treatment with s-BuLi in tetrahydrofuran (THF) at -90 degrees C has been analyzed by deuterium-labeling and natural abundance multinuclear magnetic resonance ((1)H, (2)H, (7)Li, (13)C, (31)P) studies. In the absence of coordinating cosolvents such as hexamethylphosphoramide (HMPA), eight major anionic species were identified, which allowed us to unravel the pathway of the metalation reaction. In agreement with the complex-induced proximity effect (CIPE) mechanism, the sequence of transformations emerging from this study involves the coordination of the lithium base to the P=O group of 1 to give four dimeric precomplexes whose NMR data are consistent with structures Va/Vb and VIIIa/VIIIb. The diastereomers Va/Vb are the precursors of the monomeric benzylic anion II, whereas the VIIIa/VIIIb diastereomers are assumed to undergo ortho deprotonation leading to anions I. Translocation from the ortho anion to the benzylic one is not observed. Intramolecular conjugate addition of anion II to the P-phenyl rings happens in a reversible way, affording the monomeric dearomatized anions III, IV, VI, and VII. The reaction progresses to yield a mixture containing only the species I, III, and IV. HMPA acts as a catalyst for the ortho-to-benzylic translocation and anionic cyclization reactions. Two-dimensional (2D) (7)Li,(31)P[(1)H] shift correlations and (7)Li[(31)P] NMR spectra proved to be crucial for the structural assignment of the anionic species. These techniques also demonstrated the diastereotopicity of the two achiral ligands involved in a dimer with s-BuLi (Vb) owing to the slow configuration inversion of the carbanion center.

Journal Article↗