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PubMed2002

Synthesis of isoquinolines and pyridines by the palladium/copper-catalyzed coupling and cyclization of terminal acetylenes and unsaturated imines: the total synthesis of decumbenine B.

Monosubstituted isoquinolines and pyridines have been prepared in good to excellent yields via coupling of terminal acetylenes with the tert-butylimines of o-iodobenzaldehydes and 3-halo-2-alkenals in the presence of a palladium catalyst and subsequent copper-catalyzed cyclization of the intermediate iminoalkynes. In addition, isoquinoline heterocycles have been prepared in excellent yields via copper-catalyzed cyclization of iminoalkynes. The choice of cyclization conditions is dependent upon the nature of the terminal acetylene that is employed, as only aryl and alkenyl acetylenes cyclize under the palladium-catalyzed reaction conditions that have been developed. However, aryl-, vinylic-, and alkyl-substituted acetylenes undergo palladium-catalyzed coupling and subsequent copper-catalyzed cyclization in excellent yields. The total synthesis of the isoquinoline natural product decumbenine B has been accomplished in seven steps and 20% overall yield by employing this palladium-catalyzed coupling and cyclization methodology.

Journal Article↗

PubMed2002

A study of aryl radical cyclization in enaminone esters.

Aryl radical cyclization in N-phenyl, N-benzyl, and N-phenethyl enaminone esters 1a-f was studied. N-Benzyl and N-phenethyl enaminones afforded 5-exo and 6-exo cyclization products, respectively, but radical cyclization did not occur in N-phenyl enaminones. The rate constants for the 5-exo and 6-exo cyclization processes in secondary enaminones were estimated as being on the order of 10(7) s(-1) at 353 K; since DNMR experiments showed the rate constant for rotation around the enaminone C3-N bond to be on the order of 10(4) s(-1) at this temperature, the initial enaminone configuration is maintained throughout the cyclization process. PM3 calculations suggested that the nonoccurrence of endo and 4-exo cyclizations is due to the corresponding transition structures involving significant distortion of the conjugated enaminone system.

Journal Article↗

PubMed2000

Oxyanion-accelerated C2-C6 cyclization of benzannulated enyne-allenes

The cyclization of oxyanion-substituted, benzannulated enyne-allenes was found to proceed rapidly and efficiently at room temperature, producing substituted indanones and fluorenones through a C2-C6 cyclization pathway. These reactions bear close resemblance to thermal C2-C6 cyclizations of enyne-allenes previously reported by Schmittel and others, though the oxyanion-substituted cases cyclize far more rapidly, and stand in noteworthy contrast to the C2-C7 (Myers) cyclization of (Z)-1,2,4-heptatrien-6-yne, the parent enyne-allene. The rate of reaction was found to be sensitive to the size of the alkyne and allene substituents, though the electronic effects of substitution are not known. The acceleration imparted by the oxyanion substituent is consistent with the electronic stabilization of a proposed diradicaloid transition state for the C2-C6 cyclization, but the available evidence does not permit the distinction between concerted and stepwise mechanisms. Studies are ongoing to further elucidate the mechanism and expand the scope of these transformations.

Journal Article↗

PubMed1991

Effects of temperature on excluded volume-promoted cyclization and concatemerization of cohesive-ended DNA longer than 0.04 Mb.

The 0.048502 megabase (Mb), primarily double-stranded DNA of bacteriophage lambda has single-stranded, complementary termini (cohesive ends) that undergo either spontaneous intramolecular joining to form open circular DNA or spontaneous intermolecular joining to form linear, end-to-end oligomeric DNAs (concatemers); concatemers also cyclize. In the present study, the effects of polyethylene glycol (PEG) on the cyclization and concatemerization of lambda DNA are determined at temperatures that, in the absence of PEG, favor dissociation of cohesive ends. Circular and linear lambda DNA, monomeric and concatemeric, are observed by use of pulsed field agarose gel (PFG) electrophoresis. During preparation of lambda DNA for these studies, hydrodynamic shear-induced, partial dissociation of joined cohesive ends is fortuitously observed. Although joined lambda cohesive ends progressively dissociate as their temperature is raised in the buffer used here (0.1 M NaCl, 0.01 M sodium phosphate, pH 7.4, 0.001 M EDTA), when PEG is added to this buffer, raising the temperature sometimes promotes joining of cohesive ends. Conditions for promotion of primarily either cyclization or concatemerization are described. Open circular DNAs as long as a 7-mer are produced and resolved. The concentration of PEG required to promote joining of cohesive ends decreases as the molecular weight of the PEG increases. The rate of cyclization is brought, the first time, to values that are high enough to be comparable to the rate observed in vivo. For double-stranded DNA bacteriophages that have a linear replicative form of DNA (bacteriophage T7, for example), a suppression, sometimes observed here, of cyclization mimics a suppression of cyclization previously observed in vivo. The PEG, temperature effects on DNA joining are explained by both the excluded volume of PEG random coils and an increase in this excluded volume that occurs when temperature increases.

Bacteriophage lambda↗

PubMed1982

High performance liquid chromatographic assay of cyclization activity in cell-free systems from Streptomyces clavuligerus.

A thirteen-fold excess of dithiothreitol maintains delta-(L-alpha-aminoadipyl)-L-cysteinyl-D-valine (ACV) in its monomeric form under the conditions normally encountered in an ACV cyclization assay system, using Streptomyces clavuligerus. A reversed phase high performance liquid chromatographic (HPLC) system which separates ACV monomer from isopenicillin N, penicillin N and from other cyclization assay components has been developed as follows; mobile phase: 5% methanol-95% KH2PO4 (0.05 M adjusted to pH 4.0 with concentrated H3PO4; stationary phase: muBondapak-C18; flow rate: 2 ml/minute for 5 minutes, 3 ml/minute for the remainder; detection: 220 nm). Under these conditions, authentic samples of isopenicillin N and penicillin N elute with a retention time of 5.25 minutes, which coincides with a peak of newly-formed material observed in cyclization reaction mixtures. The combined concentration of isopenicillin N and penicillin N[(iso)penicillin N] in cyclization reaction mixtures corresponds closely to the concomitant decrease in the ACV monomer. Cyclization reaction mixtures, in which crude cell-free extract from S. clavuligerus NRRL 3585 is the enzyme source, contain (iso)penicillin N at a concentration of 43.3 micrograms/ml after a 1-hour incubation period. Cyclization reaction mixtures, in which salt-precipitated cell-free extract from S. clavuligerus is the enzyme source, contain 39.0 micrograms/ml (iso)penicillin N.

Anti-Bacterial Agents↗

PubMed1994

Proteolytic excision and in situ cyclization of a bioactive loop from an REI-VL presentation scaffold.

Covalent cyclization of peptides is an important tool in structure-function analysis of bioactive peptides, because it constrains the molecule to enrich or exclude the receptor-bound conformation. Previously we described a 2-step procedure for cyclizing purified, native peptides in aqueous solution by reacting a Met or Lys side chain with an iodoacetylated N-terminus (Wood SJ, Wetzel R, 1992a, Int J Pept Protein Res 39:533-539). We show here that the cyclization reaction scheme can be extended to peptides excised from proteins by endo-LysC proteolysis, which generates fragments terminating with Lys. To illustrate the method, we used an immunoglobulin VL domain (REI-VL) with an RGD-containing sequence engineered into its CDR3 and flanked by Lys residues. This REI-VL/RGD hybrid displayed an IC50 of 24 nM for ligand competition at the platelet fibrinogen receptor alpha IIb beta 3. The RGD-containing peptide excised by endo-LysC from the REI-VL presentation scaffold exhibited an IC50 of about 50 nM, and the corresponding cyclized peptide, and IC50 of about 10 nM. Significantly, both the N alpha-acylation and the cyclization reactions occur efficiently even in the context of the other endo-LysC fragments of REI-VL, which suggests that the reaction may prove useful in converting mixtures of endo-LysC products of many proteins into the corresponding cyclic peptides in situ.

Acetylation↗

PubMed2001

Consecutive carbon-carbon bond formation approach in tandem cyclization reactions.

The conventional tandem cyclization reactions involve the formation of alternating carbon-carbon bonds, whereas the newly developed cyclization reactions involve the formation of consecutive carbon-carbon bonds, in which N-aziridinylimines have been utilized as geminal radical acceptor and donor equivalents in a single operation. This unprecedented tandem cyclization approach becomes feasible by the successful generation of 5- and 6-membered ring radicals by radical cyclizations of N-aziridinylimines. The same notion can be applied to the anionic cyclizations of N-aziridinylimines, thereby allowing anionic consecutive carbon-carbon bond formation. This approach has great synthetic potential, particularly for the construction of quaternary carbon centers, and it provides highly efficient routes for the synthesis of natural products.

Aziridines↗

PubMed1980

[Kinetic studies of the (1 linked to 4)-alpha-D-glucopyranosyltransferase reaction catalyzed by cyclodextrin glycosyltransferase, particularly the cyclization with (1 linked to 4)-alpha-D-glucopyranosyl chains (average polymerization of 16) as substrate].

The transfer reactions, particularly the cyclization reaction, catalyzed by the cyclodextrin glycosyltransferase ((1 leads to 4)-alpha-D-glucan:[(1 leads to 4)-alpha-D-glucopyranosyl]-transferase (cyclizing), EC 2.4.1.19; CGT) from Klebsiella pneumoniae M 5 al were studied with (1 leads to 4)-alpha-D-glucopyranosyl chains (d.p. 16). The initial rate of the cyclization reaction with substrate concentrations from 1 up to 16 mM indicated a V of 6.2 kat . kg-1 of protein and a molar catalytical activity of 421.6 kat . mol-1 of enzyme. Km was found to be 1.03 mM. In addition to the cyclization, CGT simultaneously catalyzed a disproportionation of the substrate, yielding shorter maltooligosaccharides and (1 leads to 4)-alpha-D-glucopyranosyl chains which were significantly longer than the substrate itself. Cyclohepta- and cycloocta-amylose were accumulated in the course of longer incubation. They arose mainly from coupling reactions with the initially formed cyclohexaamylose and corresponding disproportionation of these transfer products. The extremely low formation rates of the higher cyclodextrins point to a "mistake" of the enzyme, when cyclizing to cyclohepta- and cyclooctaamylose.

Cyclization↗

PubMed2002

Involvement of NADPH in the cyclization reaction of carotenoid biosynthesis.

Cyclic carotenoids, e.g. beta-carotene, are formed by cyclization of an acyclic precursor, lycopene. The gene, crtY, which encodes lycopene beta-cyclase, has a partial sequence characteristic of a pyridine nucleotide binding domain, and NAD(P)H has been reported to be an absolute requirement for the cyclization reaction in vitro. By complementary incubations with lycopene as substrate and with (4R)-[4-(2)H]NADPH in (1)H(2)O or with unlabelled NADPH in (2)H(2)O in the presence of the purified enzyme, it has now been shown that the hydrogen atom introduced at C(2) in the cyclization comes from water and not from NADPH. The previously proposed mechanism involving the initiation of cyclization by H(+) attack at C(2) of the folded acyclic end group of the precursor is thus confirmed. No hydrogen is transferred from NADPH, which is therefore not involved directly in the cyclization reaction, but must play an indirect role, e.g. as an allosteric activator.

Allosteric Regulation↗

PubMed2003

Effect of backbone cyclization on protein folding stability: chain entropies of both the unfolded and the folded states are restricted.

Circular versions of a large number of proteins have been designed by connecting the N and C termini via peptide linkers. A motivation for these designs is the assumed enhancement in folding stability, because backbone cyclization reduces the chain entropy of the unfolded state. Here, it is recognized that backbone cyclization also reduces the chain entropy of a flexible peptide linker in the folded state. Specifically, the end-to-end distance of the linker is restricted to fluctuations around the average displacement between the N and C termini of the folded protein. The balance of the chain-entropy reductions in the folded and unfolded states is used to predict the change in the unfolding free energy, deltadeltaG(cycl), by backbone cyclization. Predicted values of deltadeltaG(cycl) are in quantitative agreement with results of a careful study on cyclizing the 34 residue PIN1 WW domain by linkers with two to seen residues. The experimental results of an optimal linker length l=4 and a maximum stabilization of 1.7 kcal/mol are reproduced. Calculations of deltadeltaG(cycl) for a broad selection of circular proteins suggest that the stabilizing effect of backbone cyclization is modest, reflecting entropy reductions in both the unfolded and the folded states.

Animals↗

PubMed2002

Intein-mediated cyclization of a soluble and a membrane protein in vivo: function and stability.

Cyclized subunits of the E. coli glucose transporter were produced in vivo by intein mediated trans-splicing. IIA(Glc) is a beta-sandwich protein, IICB(Glc) spans the membrane eight times. Genes encoding the circularly permuted precursors U(Cdelta)-IIA(Glc)-U(Ndelta) and U(Cdelta)-IICB(Glc)-U(Ndelta) were assembled from DNA fragments encoding the 3' and 5' segments of the recA intein of M. tuberculosis and crr and ptsG of E. coli, respectively. A 20-residues long, Ala-Pro rich linker peptide and/or a histidine tag were used to join the native N- and C-termini in the cyclized proteins. The cyclized proteins complemented growth of glucose auxotrophic strains. Purified, cyclized IIA(Glc) and IICB(Glc) had 100 and 25%, respectively, of wild-type glucose phosphotransferase activity. They had an increased electrophoretic mobility, which decreased upon linearization of the proteins with chymotrypsin. Cyclized IIA(Glc) displayed increased stability against temperature and GuHCl-induced unfolding (75 vs. 70 degrees C; 1.52 vs. 1.05 M).

Cyclization↗

PubMed2000

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.

Alkenes↗

PubMed2002

Oxidative cyclization based on reversing the polarity of enol ethers and ketene dithioacetals. Construction of a tetrahydrofuran ring and application to the synthesis of (+)-nemorensic Acid.

The utility of oxidative cyclization reactions for the construction of tetrahydrofuran rings has been examined. In these experiments, alcohol nucleophiles were found to be effective traps for radical cation intermediates generated from both enol ether and ketene dithioacetal groups. The reactivity of the alcohol trapping group appeared to lie between that of an enol ether and an allylsilane trapping group. The stereochemical outcome of cyclization reactions originating from the oxidation of an enol ether was found to be controlled by stereoelectronic factors. The utility of these cyclization reactions was illustrated with the synthesis of a key tetrahydrofuran building block for the synthesis of linalool oxide and rotundisine. Cyclization reactions triggered by the oxidation of a ketene dithioacetal led to far greater levels of stereoselectivity. The stereochemical outcome of these reactions was shown to arise from steric factors involving the larger ketene acetal group. The synthetic utility of cyclizations utilizing ketene dithioacetal derived radical cations was demonstrated by completing an asymmetric synthesis of (+)-nemorensic acid. Finally, the reactions were shown to be compatible with the use of an amide nucleophile and the direct formation of a lactone product.

Acetals↗

PubMed2005

A general route for post-translational cyclization of mRNA display libraries.

Cyclic peptides are attractive scaffolds for the design of conformationally constrained molecular therapeutics. Previously, biological display libraries could only be cyclized via disulfide bonds, which are labile and can be reduced in an intracellular environment. In this paper, we construct high diversity, covalently cyclized mRNA display libraries (>1013 sequences) and analyze the cyclization reaction using MALDI-TOF MS and unnatural amino acid incorporation. Our route allows the extent of cyclization to be evaluated quantitatively and is broadly applicable to a variety of cyclization chemistries.

Cyclization↗

PubMed2006

Mechanism of wine lactone formation: demonstration of stereoselective cyclization and 1,3-hydride shift.

The cyclization mechanism of (E)-2,6-dimethyl-6-hydroxyocta-2,7-dienoic acid to wine lactone under acidic aqueous conditions was investigated using the two stereoselectively deuterium-labeled precursors (2E,6R,7Z)-[8-2H]-2,6-dimethyl-6-hydroxyocta-2,7-dienoic acid and (2E,7E)-(+/-)-[8-2H]-2,6-dimethyl-6-hydroxyocta-2,7-dienoic acid. A detailed analysis of the generated wine lactone isomers by enantioselective multidimensional gas chromatography (MDGC)/ion trap tandem mass spectrometry demonstrates that the formation of wine lactone proceeds via a nonenzymatic stereoselective cationic cyclization cascade that includes a 1,3-hydride shift. Usually, such mechanisms are features of cyclization reactions that are catalyzed by terpene cyclases. This nonenzymatic conversion of an acyclic precursor to a bicyclic monoterpene under relevant cationic cyclization conditions has rarely been observed and confirms recent suggestions that the precursor itself can provide the chemical functionality required for specific steps in the cyclization cascade.

Cyclization↗

PubMed2000

Isothermal Fourier transform infrared microspectrosopic studies on the stability kinetics of solid-state intramolecular cyclization of aspartame sweetener.

A novel Fourier transform infrared (FT-IR) microspectrophotometer equipped with differential scanning calorimetry (DSC) was used to investigate the kinetics of intramolecular cyclization of aspartame (APM) sweetener in the solid state under isothermal conditions. The thermal-dependent changes in the peak intensity of IR spectra at 1543, 1283, and 1259 cm(-1) were examined to explore the reaction. The results support that the intramolecular cyclization process in APM proceeded in three steps: the methoxyl group of ester was first thermolyzed to release methanol, then an acyl cation was attacked by the lone pair of electrons available on nitrogen by an S(N)1 pathway, and finally ring-closure occurred. The intramolecular cyclization of APM determined by this microscopic FT-IR/DSC system was found to follow zero-order kinetics after a brief induction period. The bond cleavage energy (259.38 kJ/mol) of thermolysis for the leaving group of -OCH(3), the bond conversion energy (328.88 kJ/mol) for the amide II NH band to DKP NH band, and the CN bond formation energy (326.93 kJ/mol) of cyclization for the DKP in the APM molecule were also calculated from the Arrhenius equation. The total activation energy of the DKP formation via intramolecular cyclization was 261.33 kJ/mol, calculated by the above summation of the bond energy of cleavage, conversion, and formation, which was near to the value determined by the DSC or TGA method. This indicates that the microscopic FT-IR/DSC system is useful as a potential tool not only to investigate the degradation mechanism of drugs in the solid state but also to directly predict the bond energy of the reaction.

Aspartame↗

PubMed2002

Short and stereoselective total synthesis of furano lignans (+/-)-dihydrosesamin, (+/-)-lariciresinol dimethyl ether, (+/-)-acuminatin methyl ether, (+/-)-sanshodiol methyl ether, (+/-)-lariciresinol, (+/-)-acuminatin, and (+/-)-lariciresinol monomethyl ether and furofuran lignans (+/-)-sesamin, (+/-)-eudesmin, (+/-)-piperitol methyl ether, (+/-)-pinoresinol, (+/-)-piperitol, and (+/-)-pinoresinol monomethyl ether by radical cyclization of epoxides using a transition-metal radical source.

Intramolecular radical cyclization of suitably substituted epoxy ethers 4a-g using bis(cyclopentadienyl)titanium(III) chloride as the radical source resulted in trisubstituted tetrahydrofurano lignans and 2,6-diaryl-3,7-dioxabicyclo[3.3.0]octane lignans depending on the reaction conditions. The titanium(III) species was prepared in situ from commercially available titanocene dichloride and activated zinc dust in THF. Upon radical cyclization followed by acidic workup, epoxy olefinic ethers 4a-g afforded furano lignans dihydrosesamin 1a, lariciresinol dimethyl ether 1b, acuminatin methyl ether 1e, and sanshodiol methyl ether 1g directly and lariciresinol 1h, acuminatin 1i, and lariciresinol monomethyl ether 1j after removal of the benzyl protecting group by controlled hydrogenolysis of the corresponding cyclized products. The furofuran lignans sesamin 2a, eudesmin 2b, and piperitol methyl ether 2e were also prepared directly by using the same precursors 4a-f on radical cyclization followed by treatment with iodine and pinoresinol 2h, piperitol 2i, and pinoresinol monomethyl ether 2j after controlled hydrogenolysis of the benzyl protecting group of the corresponding cyclized products. Two naturally occurring acyclic lignans, secoisolariciresinol 5h and secoisolariciresinol dimethyl ether 5b, have also been prepared by exhaustive hydrogenolysis of 2h and 2b, respectively.

Alkylation↗

PubMed2002

Nitrile anions: solvent-dependent cyclizations.

Extensive cyclizations in hydrocarbon and polar solvents demonstrate a profound solvent sensitivity for intramolecular nitrile anion alkylations. S(N)i cyclizations enforce very precise steric constraints in the transition state, allowing correlation of the cyclization stereochemistry with the orbital orientation of the nitrile anion. Collectively the cyclizations suggest a continuum of nitrile anion transition states, varying from planar to fully pyramidal, that selectively cyclize to cis- and trans-decalins, respectively.

Anions↗