Herman J. C. Yeh

Investigation of the TCA cycle and the glyoxylate shunt in Escherichia coli BL21 and JM109 using 13C‐NMR/MS

Acetate accumulation is a common problem observed in aerobic high cell density Escherichia coli cultures. A previous report has hypothesized that the glyoxylate shunt is active in a low acetate producer, E. coli BL21, and inactive in a high acetate producer, JM109. To further investigate this hypothesis, we now develop a model for the incorporation of 13C from uniformly labeled glucose into key TCA cycle intermediates. The 13C isotopomer distributions of oxaloacetate and acetyl‐CoA are first determined using NMR and MS techniques. These distributions are next validated by predicting the NMR spectrum of glutamate. Under steady state isotopic conditions, and with knowledge of the full isotopomer distributions of oxaloacetate and acetyl‐CoA, the flux ratios through the TCA cycle and the glycoxylate shunt are obtained with respect to the flux through the PPC anaplerotic shunt. We conclude that in BL21, the glyoxylate shunt is active at 22% of the flux through the TCA cycle, and is inactive in JM109. Further, in BL21, the flux through the TCA cycle equals the flux through the PPC shunt, while in JM109 the TCA cycle flux is only third of the flux through the PPC shunt.

Phantasmidine: an epibatidine congener from the ecuadorian poison frog Epipedobates anthonyi.

The skin of the Ecuadorian poison frog Epipedobates anthonyi contains the potent nicotinic agonists epibatidine (1) and N-methylepibatidine (3). In addition, a condensed tetracyclic epibatidine congener has been identified with activity at nicotinic acetylcholine receptors, but different selectivity than epibatidine. This rigid tetracycle has been named phantasmidine (4). Phantasmidine has a molecular formula of C(11)H(11)N(2)OCl, shares a chloropyridine moiety with 1, and also contains furan, pyrrolidine, and cyclobutane rings. A combination of GC-MS and GC-FTIR analysis with on-column derivatization, 1D NMR spectroscopy with selective irradiation, and spectral simulation, along with 2D NMR, were used to elucidate the structure from a total sample of approximately 20 microg of HPLC-purified 4 and its corresponding acetamide (5). After synthesis, this novel rigid agonist may serve as a selective probe for beta4-containing nicotinic receptors and potentially lead to useful pharmaceuticals.

Structures of covalent nucleoside adducts formed from adenine, guanine, and cytosine bases of DNA and the optically active bay-region 3,4-diol 1,2-epoxides of benz[a]anthracene

Chemical structures of the principal covalent adducts formed from DNA upon reaction in vitro with the four optically active 3,4-diol 1,2-epoxides of benz[a]anthracene have been elucidated at the nucleoside level. In addition to adducts formed by cis and trans addition of the exocyclic amino groups of deoxyadenosine (dA) and deoxyguanosine (dG) and a trans deoxycytidine (dC) adduct, chemical characterization of a deglycosylated N-7 dG adduct formed in DNA by trans opening of the (4S,3R)-diol (2R,IS)-epoxide isomer is reported. Relative stereochemistries of the adducts (cis versus trans opening of the epoxides by the exocyclic amino groups) were deduced from the coupling constants of the methine protons of the tetrahydro benzo rings of the acetylated derivatives

Absolute configuration of the 5,6-oxide formed from 7,12-dimethylbenz[a]anthracene by cytochrome P450c

The absolute configurations of the enantiomeric 5,6-arene oxides of 7,12-dimethylbenz[a]anthracene (DMBA) were recently assigned such that the late eluting enantiomer from a chiral HPLC column has 5R,6S absolute configuration. [Mushtaq et al. (1984) BBRC 125, 539]. The authors further concluded that the 5R,6S-enantiomer predominates on metabolism of DMBA by cytochrome P450c in liver microsomes from 3-methylcholanthrene-treated rats. Their chemical assignment of absolute configuration is incorrect. Thus, metabolism of DMBA by these microsomes as well as by homogeneous cytochrome P450c produces 5,6-oxide highly enriched (95%) in the 5S,6R-enantiomer in accord with theoretical predictions.

Tandem silica gel-catalysed rearrangements and subsequent Baeyer–Villiger reactions of artemisinin derivatives

Novel silica gel-catalysed reactions of dihydroartemisinin 1b to deoxyartemisinin 11 and 11β-hydroxy-11-epidihydroartemisinin 8 to compound 9 under mild conditions are described. The structures of the products were determined by mass spectrometry and 1D- and 2D-NMR spectroscopy. A mechanism for their formation is proposed.

Synthesis of deoxyadenosine adducts from the highly carcinogenic fjord region diol epoxide of benzo[c]phenanthrene

Abstract Unlike bay-region diol epoxides, the fjord-region benzo[c]phenanthrene 3,4-diol 1,2-epoxide-2(4-hydroxyl and epoxide oxygen trans) undergoes non-regioselective ring opening by both ammonia and azide anion. Adducts corresponding to a benzylic and non-benzylic SN2 ring opening by N6 of deoxyadenosine have been characterized.

NMR Conformational Analysis of DNA Duplexes Containing Diol Epoxide Adducts of Polycyclic Aromatic Hydrocarbons

Abstract The principal adducts formed between DNA and polycyclic aromatic hydrocarbon diol epoxides result from N-alkylation of the exocyclic amino groups of the purine bases by the benzylic carbon atom of the epoxide. To date, the solution conformations of more than a dozen alkylated DNA duplexes have been examined by 2D NMR spectroscopy. For trans opened diol epoxides, oligomer duplexes containing N2-adducts at deoxyguanosine have the hydrocarbon residue lying in the minor groove whereas those containing N6-adducts at deoxyadenosine have the hydrocarbon intercalated within the DNA helix. Absolute configuration at the site of attachment appears to be a major determinant in establishing whether the hydrocarbon lies to the 3′- or the 5′-side of the adducted base. For trans opened deoxyadenosine adducts with R-absolute configuration, the hydrocarbon residue is positioned toward the 5′-end of the adducted strand whereas trans opened deoxyguanosine adducts with R-absolute configuration have the hydrocarbon lo...

Effect of Absolute Configuration on the Optical and NMR Properties of Oligonucleotides Containing Benzo[a]Pyrene Adducts at N 6 of Deoxyadenosine

Abstract For oligonucleotide duplexes derived from trans opening of benzo[a]pyrene diol epoxides (BaP DEs) by the exocyclic N6-amino group of deoxyadenosine (dA), the hydrocarbon is intercalated toward the 5′-end of the modified strand when the configuration at the site of attachment of the base to the hydrocarbon (C-10) is R, and toward the 3′-end when this configuration is S. In oligonucleotide 11-mer duplexes modified by BaP DE-1 (benzylic 7-OH and epoxide oxygen cis) and DE-2 (7-OH and epoxide oxygen trans), as well as 7,8,9,10-tetrahydro BaP 9,10-epoxide, 10R adducts had consistently higher (5–9d°C) Tm values than the corresponding 10S adducts. Dodecamer duplexes from the HPRT gene with trans opened 10S (but not those with 10R) BaP DE-2 adducts at either of two adjacent dA residues exhibited blue shifts at ∼350 nm at temperatures well below the Tm. We propose that these blue shifts result from a conformation in which the hydrocarbon is not stacked with the DNA bases.