N-Substituted Derivatives of the Azadithiolate Cofactor from the [FeFe] Hydrogenases: Stability and Complexation

Experiments are described that probe the stability of N-substituted derivatives of the azadithiolate cofactor recently confirmed in the [FeFe] hydrogenases (Berggren, G., et al. Nature 2013, 499, 66). Acid-catalyzed hydrolysis of bis(thioester) BnN(CH2SAc)2 gives [BnNCH2SCH2]2 rather than azadithiol BnN(CH2SH)2. Treatment of BnN(CH2SAc)2 with NaO(t)Bu generates BnN(CH2SNa)2, which was trapped with NiCl2(diphos) (diphos = 1,2-C2H4(PR2)2; R = Ph (dppe) and Cy (dcpe)) to give fully characterized complexes Ni[(SCH2)2NBn](diphos). The related N-aryl derivative Ni[(SCH2)2NC6H4Cl](diphos) was prepared analogously from 4-ClC6H4N(CH2SAc)2, NaO(t)Bu, and NiCl2(dppe). Crystallographic analysis confirmed that these rare nonbridging [adt(R)](2-) complexes feature distorted square planar Ni centers. The analogue Pd[(SCH2)2NBn](dppe) was also prepared. (31)P NMR analysis indicates that Ni[(SCH2)2NBn](dppe) has basicity comparable to typical amines. As shown by cyclic voltammetry, the couple [M[(SCH2)2NBn](dppe)](+/0) is reversible near -2.0 V versus Fc(+/0). The wave shifts to -1.78 V upon N-protonation. In the presence of CF3CO2H, Ni[(SCH2)2NBn](dppe) catalyzes hydrogen evolution at rate of 22 s(-1) in the acid-independent regime, at room temperature in CH2Cl2 solution. In contrast to the instability of RN(CH2SH)2 (R = alkyl, aryl), the dithiol of tosylamide TsN(CH2SH)2 proved sufficiently stable to allow full characterization. This dithiol reacts with Fe3(CO)12 and, in the presence of base, NiCl2(dppe) to give Fe2[(SCH2)2NTs](CO)6 and Ni[(SCH2)2NTs](dppe), respectively.

A roadmap to the isotopolog space of flavocoenzymes

Flavocoenzymes with selective or universal stable isotope labeling are important tools for the investigation of flavoproteins using a variety of spectroscopic methods. Numerous selectively labeled flavin isotopologs can be generated by the combined application of chemical synthesis and in vitro biotransformation using commercially available enzymes and/or recombinant riboflavin biosynthesis enzymes. Notably, the complex reaction sequences can be rapidly carried out using enzyme-assisted one-pot reaction strategies.

Enhancing Regiocontrol in Carboaluminations of Terminal Alkynes. Application to the One-Pot Synthesis of Coenzyme Q10

Two new "generations" of methodological advances are reported for the Negishi carboalumination of terminal alkynes. Use of simple, inexpensive additives that alter the Al-Zr complex formed between Me(3)Al and Cp(2)ZrCl(2) give rise to an especially effective reagent mix that results in virtually complete control of regiochemistry upon carboalumination of 1-alkynes. One timely application to coenzyme Q10 is highlighted. Regioisomers from subsequent coupling, which would otherwise be very difficult to separate, are avoided.

Kinetic Analysis of Semisynthetic Peroxidase Enzymes Containing a Covalent DNA–Heme Adduct as the Cofactor

The reconstitution of apo enzymes with DNA oligonucleotide-modified heme (protoporphyrin IX) cofactors has been employed as a tool to produce artificial enzymes that can be specifically immobilized at the solid surfaces. To this end, covalent heme-DNA adducts were synthesized and subsequently used in the reconstitution of apo myoglobin (aMb) and apo horseradish peroxidase (aHRP). The reconstitution produced catalytically active enzymes that contained one or two DNA oligomers coupled to the enzyme in the close proximity to the active site. Kinetic studies of these DNA-enzyme conjugates, carried out with two substrates, ABTS and Amplex Red, showed a remarkable increase in peroxidase activity of the DNA-Mb enzymes while a decrease in enzymatic activity was observed for the DNA-HRP enzymes. All DNA-enzyme conjugates were capable of specific binding to a solid support containing complementary DNA oligomers as capture probes. Kinetic analysis of the enzymes immobilized by the DNA-directed immobilization method revealed that the enzymes remained active after hybridization to the capture oligomers. The programmable binding properties enabled by DNA hybridization make such semisynthetic enzyme conjugates useful for a broad range of applications, particularly in biocatalysis, electrochemical sensing, and as building blocks for biomaterials.

Direct transfer of extended groups from synthetic cofactors by DNA methyltransferases

S-Adenosyl-L-methionine (AdoMet) is the major methyl donor for biological methylation reactions catalyzed by methyltransferases. We report the first chemical synthesis of AdoMet analogs with extended carbon chains replacing the methyl group and their evaluation as cofactors for all three classes of DNA methyltransferases. Extended groups containing a double or triple bond in the beta position to the sulfonium center were transferred onto DNA in a catalytic and sequence-specific manner, demonstrating a high utility of such synthetic cofactors for targeted functionalization of biopolymers.

Microscale synthesis of isotopically labeled R-[6-xH]N5,N10-methylene-5,6,7,8-tetrahydrofolate as a cofactor for thymidylate synthase

A one-pot synthesis of isotopically labeled R-[6-xH]N5,N10-methylene-5,6,7,8-tetrahydrofolate (CH2H4F) is presented, where x=1, 2, or 3 represents hydrogen, deuterium, or tritium, respectively. The current procedure offers high-yield, high-purity, and microscale-quantity synthesis. In this procedure, two enzymes were used simultaneously in the reaction mixture. The first was Thermoanaerobium brockii alcohol dehydrogenase, which stereospecifically catalyzed a hydride transfer from C-2-labeled isopropanol to the re face of oxidized nicotinamide adenine dinucleotide phosphate to form R-[4-xH]-labeled reduced nicotinamide adenine dinucleotide phosphate. The second enzyme, Escherichia coli dihydrofolate reductase, used the xH to reduce 7,8-dihydrofolate (H2F) to form S-[6-xH]5,6,7,8-tetrahydrofolate (S-[6-xH]H4F). The enzymatic reactions were followed by chemical trapping of S-[6-xH]H4F with formaldehyde to form the final product. Product purification was carried out in a single step by reverse phase high-pressure liquid chromatography separation followed by lyophilization. Two analytical methods were developed to follow the reaction progress. Finally, the utility of the labeled cofactor in mechanistic studies of thymidylate synthase is demonstrated by measuring the tritium kinetic isotope effect on the enzyme's second order rate constant.

Synthesis of Imidazolo Analogues of the Oxidation−Reduction Cofactor Pyrroloquinoline Quinone (PQQ)

Parallel syntheses of 2-hydro-, 2-methyl-, and 2-methoxycarbonylimidazo-7,9-dimethoxycarbonyl analogues of the oxidation-reduction cofactor pyrroloquinoline quinone [4,5-dihydro-4,5-dioxo-1H-pyrrolo[2,3-f]quinoline-2,7,9-tricarboxylic acid] have been developed. The properties of the imidazolo analogues in relation to the corresponding pyrrole analogues will be important in assessing the origins of catalysis and biological activity in the cofactor, which has recently been shown to be a vitamin.

Transglutaminase-catalyzed synthesis of trypsin-cyclodextrin conjugates: kinetics and stability properties

Bovine pancreatic trypsin was modified by the mono-6-amino-6-deoxy derivatives of alpha-, beta-, and gamma-cyclodextrin through a transglutaminase-catalyzed reaction. The trypsin-cyclodextrin conjugates, containing about 3 mol of oligosaccharide per mole of protein, were tested for their catalytic and stability properties. The specific esterolytic activity and the kinetics constants of trypsin were significantly improved following the transglutaminase-induced structural modifications. Trypsin-cyclodextrin conjugates were also found markedly (sixfold) more resistant to autolytic degradation at alkaline pH, and their thermal stability profile was improved by about 16 degrees C. Moreover, they were particularly resistant to heat inactivation when treated at different temperatures ranging from 45 degrees C to 70 degrees C for different periods of time.

3,4-(4-Methoxybenzo):8,9-benzobicyclo[4.4.1]undeca-3,8-dien-11-one ethylene acetal

The title compound, 5-methoxyspiro[tetracyclo[8.8.1.0(3,8).0(12,17)]nonadeca-3,5,7,12,14,16-hexene-19,2'-[1,3]dioxolane], C(22)H(24)O(3), exhibits a twin-chair conformation with the aromatic rings overlying each other. Comparison of the dihedral angle between these two rings with those from previously reported [3.3]orthocyclophanes of this type suggests the presence of a weak attractive charge-transfer interaction between the two, different, stacked arenes.

Characterization of an allylic analogue of the 5'-deoxyadenosyl radical: an intermediate in the reaction of lysine 2,3-aminomutase

An allylic analogue of the 5'-deoxyadenosyl radical has been characterized at the active site of lysine 2,3-aminomutase (LAM) by electron paramagnetic resonance (EPR) spectroscopy. The anhydroadenosyl radical, 5'-deoxy-3',4'-anhydroadenosine-5'-yl, is a surrogate of the less stable 5'-deoxyadenosyl radical, which has never been observed but has been postulated to be a radical intermediate in the catalytic cycles of a number of enzymes. An earlier communication [Magnusson, O.Th., Reed, G. H., and Frey, P. A. (1999) J. Am. Chem. Soc. 121, 9764-9765] included the initial spectroscopic identification at 77 K of the radical, which is formed upon replacement of S-adenosylmethionine by S-3',4'-anhydroadenosylmethionine as a coenzyme for LAM. The electron paramagnetic resonance spectrum of the radical changes dramatically between 77 and 4.5 K. This unusual temperature dependence is attributed to a spin-spin interaction between the radical and thermally populated, higher spin states of the [4Fe-4S]+2 center, which is diamagnetic at 4.5 K. The EPR spectra of the radical at 4.5 K have been analyzed using isotopic substitutions and simulations. Analysis of the nuclear hyperfine splitting shows that the unpaired spin is distributed equally between C5'- and C3'- as expected for an allylic radical. Hyperfine splitting from the beta-proton at C-2'(H) shows that the dihedral angle to the p(z)-orbital at C-3' is approximately 37 degrees. This conformation is in good agreement with a structural model of the radical. The rate of formation of the allylic radical shows that it is kinetically competent as an intermediate. Measurements of 2H kinetic isotope effects indicate that with lysine as the substrate, the rate-limiting steps follow initial reductive cleavage of the coenzyme analogue.

Synthesis and properties of new coenzyme mimics based on the artificial coenzyme CL4

We have previously shown that a range of nicotinamide containing 'biomimetic coenzymes' function as active analogues of NAD+ in the oxidation of alcohols by horse liver alcohol dehydrogenase (HLADH), despite their apparently astonishing lack of structural similarity to the natural coenzyme. The simplest structure as yet shown to exhibit activity is the biomimetic coenzyme CL4. To investigate the effect of the structure of this truncated artificial coenzyme on its activity, a range of close structural analogues of CL4 were designed, synthesized and characterized. The electrochemical reduction potentials of the analogues were strongly influenced by the nature of the groups attached to the pyridine ring. All of the analogues could be chemically reduced using sodium borohydride, to give compounds with altered UV-visible absorption and fluorescence properties. An HPLC-based assay suggested that two of the new analogues were coenzymically active in the oxidation of butan-1-ol by HLADH, with one displaying a significantly higher activity than CL4. The results demonstrate which features of the structures of the coenzymes lead to desirable electrochemical and spectroscopic properties, but suggest that the structural requirements for a functional coenzyme are quite stringent. These observations may be used to design an artificial coenzyme which combines the best features of those studied so far.

The design of protein-based catalysts using semisynthetic methods

The combination of site-directed mutagenesis and chemical modification has resulted in the preparation of protein conjugates with new and useful properties. Proteins modified with metal-chelating groups are proving useful for mapping tertiary and quaternary interactions using the technique of affinity cleavage. The attachment of cofactors, including pyridoxal and pyridoxamine, has resulted in the preparation of semisynthetic transaminases that display enzyme-like properties, including enantioselectivity, substrate specificity and reaction-rate acceleration.

Synthesis of esters of coenzyme PQQ and IPQ, and stimulation of nerve growth factor production

Esters of pyrroloquinoline quinone (PQQ), a cofactor of microbial quinoprotein enzyme, and imidazopyrroloquinoline (IPQ, from PQQ and glycine) were synthesized, and their chemical stability, toxicity to L-M cells and nerve growth factor (NGF) inducing activity in L-M cells were studied. PQQ esters were found to be potent enhancers of NGF production, but IPQ esters had only marginal effects on NGF production. The monoester of PQQ with a methoxycarbonyl group at C-2 of PQQ is a most effective compound because of its NGF inducing activity, limited toxicity, safety and chemical stability. These results suggest that PQQ-2-esters could be developed as a curative or preventive drug for retrograde neural diseases in the central and perpheral nervous system.

Identification of novel reduced pyridinium derivatives as synthetic co-factors for the enzyme DT diaphorase (NAD(P)H dehydrogenase (quinone), EC 1.6.99.2)

The enzyme DT diaphorase (NAD(P)H dehydrogenase (quinone), EC 1.6.99.2) is unusual in that it can utilize either NADH or NADPH as a co-factor for the reduction of its substrates. We have shown that the intact NAD(P)H molecule is not required and that other reduced pyridinium compounds can also act as co-factors for DT diaphorase. The entire adenine dinucleotide portion of NAD(P)H can be dispensed with entirely and the simplest quaternary (and therefore reducible) derivative of nicotinamide, 1-methylnicotinamide, was as effective as NAD(P)H as a co-factor for the reduction of the quinone, menadione. Nicotinamide 5'-O-benzoyl riboside was also as effective a co-factor as NAD(P)H, whilst nicotinamide ribotide and riboside have a higher Km, and decreased the kcat of DT diaphorase. Nicotinic acid derivatives had little activity. Kinetic analysis indicated that both nicotinamide ribotide and riboside may be interacting with the menadione binding site rather than the NAD(P)H site. Irrespective of the differences between the various reduced pyridinium derivatives in their ability to act as co-factors for the reduction of menadione by DT diaphorase, all the compounds that showed activity in this assay were equally effective co-factors for the reduction of the nitrobenzamide, CB 1954 (5-(aziridin-1-yl)-2,4-dinitrobenzamide). The apparent Km of DT diaphorase for all these co-factors approached zero. It was concluded that co-factor binding is not a rate-limiting step in the nitroreductase activity of DT diaphorase.

Synthesis of the coenzymes adenosine diphosphate glucose, guanosine diphosphate glucose, and cytidine diphosphoethanolamine under primitive Earth conditions

The nonenzymatic synthesis of the coenzymes adenosine diphosphate glucose (ADPG), guanosine diphosphate glucose (GDPG), and cytidine diphosphoethanolamine (CDP-ethanolamine) has been carried out under conditions considered to have been prevalent on the early Earth. The production of these compounds was performed by allowing simple precursor molecules to react under aqueous solutions, at moderate temperatures and short periods of time, with mediation by cyanamide or urea. These two condensing agents are considered to have been present in significant amounts on the primitive Earth and have been previously used in the nonenzymatic synthesis of several other important biochemical compounds. In our experiments, ADPG was obtained by heating glucose-1-phosphate (G1P) and ATP in the presence of cyanamide for 24 h at 70 degrees C. The reaction of G1P and GTP under the same conditions yielded GDPG. The cyanamide-mediated production of CDP-ethanolamine was carried out by reacting a mixture of ethanolamine phosphate and CTP for 24 h at 70 degrees C. The separation and identification of the reaction products was carried out by paper chromatography, thin-layer chromatography, high performance thin-layer chromatography, high performance liquid chromatography, both normal and reverse-phase, UV spectroscopy, enzymatic assays, and acid hydrolysis. Due to the mild conditions employed, and to the relative ease of these reactions, these studies offer a simple attractive system for the nonenzymatic synthesis of phosphorylated high-energy metabolic intermediates under conditions considered to have been prevalent on the ancient Earth.

Soybean lipoxygenases-1, -2a, -2b and -2c do not contain PQQ

Soybean isoenzymes lipoxygenases-1, -2a, -2b and -2c were examined spectroscopically for the presence of covalently bound pyrrolo quinoline quinone (PQQ) after derivatization by phenylhydrazine (PH), 2,4-dinitrophenylhydrazine (DNPH) and 3-methyl-2-benzothiazolinone hydrazone (MBTH). DNPH derivatization of PQQ after a pronase digestion step of lipoxygenase-1 in the presence of an anion exchange gel fixing the cofactor was also investigated. None of these experiments provided evidence for the presence of PQQ contrary to previous report by Van der Meer et al (1). We have checked, by EPR spectroscopy, that the three reactants used were able to reduce the active site ferric iron. Our results were confirmed by the absence of enzyme inhibition by cis- and trans-1,2-diaminocyclohexane or benzylamine in the presence of NaBH3CN which have been reported to react with PQQ and to inactivate quinoproteins (2,3).

The use of carba(dethia)-coenzyme A (CH2CoA) derivatives for mechanistic investigations

A novel class of acyl-coenzyme A analogues has been synthesized in which the sulphur atom is replaced by methylene. In contrast to their natural thiolester counterparts these acyl-CH2CoA analogues are stable to hydrolysis. They are good substrates for several enzymes that do not attack the thiolester group (carboxylases, mutases, dehydrogenases, epimerases, etc.) and potent inhibitors for most enzymes that do so. Some of the new insights gained by the use of acyl-CH2CoA are discussed in terms of enzymatic mechanisms.