James L. Alderfer

Detection of epithelial ovarian cancer using 1H-NMR-based metabonomics

Currently available serum biomarkers are insufficiently reliable to distinguish patients with epithelial ovarian cancer (EOC) from healthy individuals. Metabonomics, the study of metabolic processes in biologic systems, is based on the use of 1H‐NMR spectroscopy and multivariate statistics for biochemical data generation and interpretation and may provide a characteristic fingerprint in disease. In an effort to examine the utility of the metabonomic approach for discriminating sera from women with EOC from healthy controls, we performed 1H‐NMR spectroscopic analysis on preoperative serum specimens obtained from 38 patients with EOC, 12 patients with benign ovarian cysts and 53 healthy women. After data reduction, we applied both unsupervised Principal Component Analysis (PCA) and supervised Soft Independent Modeling of Class Analogy (SIMCA) for pattern recognition. The sensitivity and specificity tradeoffs were summarized for each variable using the area under the receiver‐operating characteristic (ROC) curve. In addition, we analyzed the regions of NMR spectra that most strongly influence separation of sera of EOC patients from healthy controls. PCA analysis allowed correct separation of all serum specimens from 38 patients with EOC (100%) from all of the 21 premenopausal normal samples (100%) and from all the sera from patients with benign ovarian disease (100%). In addition, it was possible to correctly separate 37 of 38 (97.4%) cancer specimens from 31 of 32 (97%) postmenopausal control sera. SIMCA analysis using the Coomans plot demonstrated that sera classes from patients with EOC, benign ovarian cysts and the postmenopausal healthy controls did not share multivariate space, providing validation for the class separation. ROC analysis indicated that the sera from patients with and without disease could be identified with 100% sensitivity and specificity at the 1H‐NMR regions 2.77 parts per million (ppm) and 2.04 ppm from the origin (AUC of ROC curve = 1.0). In addition, the regression coefficients most influential for the EOC samples compared to postmenopausal controls lie around δ3.7 ppm (due mainly to sugar hydrogens). Other loadings most influential for the EOC samples lie around δ2.25 ppm and δ1.18 ppm. These findings indicate that 1H‐NMR metabonomic analysis of serum achieves complete separation of EOC patients from healthy controls. The metabonomic approach deserves further evaluation as a potential novel strategy for the early detection of epithelial ovarian cancer.

Use of 1,2-dichloro 4,5-dicyanoquinone (DDQ) for cleavage of the 2-naphthylmethyl (NAP) group

Abstract The 2-naphthylmethyl (NAP) group is a versatile group for protection of hydroxyl functions. It is stable to 4% TFA in CHCl 3 , hot 80% HOAc–H 2 O, SnCl 2 –AgOTf and HCl–EtOH, but it can readily be removed with DDQ in CH 2 Cl 2 .

Solution structure of the loops of bacteriorhodopsin closely resembles the crystal structure

Bacteriorhodopsin is one of very few transmembrane proteins for which high resolution structures have been solved. The structure shows a bundle of seven helices connected by six turns. Some turns in proteins are stabilized by short range interactions and can behave as small domains. These observations suggest that peptides containing the sequence of the turns in a membrane protein such as bacteriorhodopsin may form stable turn structures in solution. To test this hypothesis, we determined the solution structure of three peptides each containing the sequence of one of the turns in bacteriorhodopsin. The solution structures of the peptides closely resemble the structures of the corresponding turns in the high resolution structures of the intact protein.

The 2-naphthylmethyl (NAP) group in carbohydrate synthesis: first total synthesis of the GlyCAM-1 oligosaccharide structures.

Total syntheses of the GlyCAM-1 (glycosylation-dependent cell adhesion molecule-1) oligosaccharide structures: [alpha-NeuAc-(2 --> 3)-beta-Gal-(1 --> 4)-[alpha-Fuc-(1 --> 3)]-beta-(6-O-SO3Na)-GlcNAc-(1 --> 6)]-[alpha-NeuAc-(2 --> 3)-beta-Gal-(1 --> 3)]-alpha-GalNAc-OMe (1) and [alpha-NeuAc-(2 --> 3)-beta-Gal-(1 --> 4)-[alpha-Fuc-(1 --> 3)]-beta-GlcNAc-(1 --> 6)]-[alpha-NeuAc-(2 3)-beta-Gal-(1 --> 3)]-alpha-GalNAc-OMe (2) through a novel sialyl LewisX tetrasaccharide donor are described. Employing sequential glycosylation strategy, the starting trisaccharide was regio- and stereoselectively constructed through coupling of a disaccharide imidate with the monosaccharide acceptor phenyl-6-O-naphthylmethyl-2-deoxy-2-phthalimido-1-thio-beta-D-glucopyranoside with TMSOTf as a catalyst without affecting the SPh group. The novel sialyl Lewisx tetrasaccharide donor 3 was then obtained by alpha-L-fucosylation of trisaccharide acceptor with the 2,3,4-tri-O-benzyl-1-thio-beta-L-fucoside donor. The structure of the novel sialyl Lewisx tetrasaccharide was established by a combination of 2D DQF-COSY and 2D ROESY experiments. Target oligosaccharides 1 and 2 were eventually constructed through heptasaccharide which was obtained by regioselective assembly of advanced sialyl Lewisx tetrasaccharide donor 3 and a sialylated trisaccharide acceptor in a predictable and controlled manner. Finally, target heptasaccharides 1 and 2 were fully characterized by 2D DQF-COSY, 2D ROESY, HSQC, HMBC experiments and FAB mass spectroscopy.

Radiation chemistry of d(TpApCpG) in oxygenated solution.

The radiation chemistry of the DNA tetranucleoside triphosphate d(TpApCpG) was investigated. The tetramer was X-irradiated in oxygenated aqueous solution and the various products separated by high-performance liquid chromatography. The principal modifications of the tetramer were analysed intact using nuclear magnetic resonance (NMR) spectroscopy and in some instances also by fast atom bombardment (FAB) mass spectrometry. The principal radiation-induced lesions of d(TpApCpG) were found to be a formamido modification derived from the thymine base, two stereoisomeric forms of a 1-carbamoyl-2-oxo-4,5-dihydroxyimidazolidine modification derived from the cytosine base and an 8-hydroxyguanine modification.

Chemical synthesis of sulfated oligosaccharides with a β-d-Gal-(1→3)-[β-d-Gal-(1→4)-(α-l-Fuc-(1→3)-β-d-GlcNAc-(1→6)]-α-d-GalNAc sequence

Abstract The syntheses of two sulfated pentasaccharides: β- d -Gal6SO 3 Na-(1→3)-[β- d -Gal-(1→4)-α- l -Fuc-(1→3)-β- d -GlcNAc-(1→6)]-α- d -GalNAc→OMe ( 1 ) and β- d -Gal6SO 3 Na-(1→3)-[β- d -Gal-(1→4)-α- l -Fuc-(1→3)-β- d -GlcNAc6SO 3 Na-(1→6)]-α- d -GalNAc→OMe ( 2 ) by using Lewis X trisaccharides 12 and 16 as glycosyl donors are described. Sulfated oligosaccharides 1 – 2 and intermediate compounds are fully characterized by 2D 1 H– 1 H DQF-COSY and 2D ROESY experiments.

Pyrazolinyl and cyclopropyl derivatives of protoporphyrin IX and chlorins related to chlorophyll a

Abstract Diazomethane reacts regioselectively with peripheral vinyl substituents of pyropheophorbide a and purpurin-18 N-methylimide to produce corresponding 1′-pyrazolinyl-substituted derivatives as a main product. Similarly, treatment of protoporphyrin IX gave a mixture of mono- and di-substituted pyrazolinyl analogs, which were isolated as individual products. Thermolytic decomposition of the pyrazolinyl derivatives produced cyclopropyl-substituted chlorins and porphyrins. 1,3-Dipolar cycloaddition mechanisms of the formation of 1′-pyrazolinyl derivatives are discussed.

Synthesis of Mono- and Di(oxopyri)porphyrins: A New Approach through Ring Enlargement with Diazomethane

A novel approach for porphyrin modification is provided by ring-enlargement reactions. Treatment of dioxochlorins (see scheme) and tetraoxobacteriochlorins with diazomethane results in formation of the corresponding mono- and di(oxopyri)porphyrins.

Total synthesis of a sialylated and sulfated oligosaccharide from O-linked glycoproteins

Abstract The total synthesis of a sialylated and sulfated oligosaccharide 1 representative of a structure occurring in respiratory mucins has been accomplished. Our strategy depends upon the employment of 2-naphthymethyl (NAP) protection for hydroxyl functions. Choice of the well-defined sialyl donor 15 was made because of its enhanced reactivity over the parent compound 14 for glycosylation.

Total synthesis of sialylated and sulfated oligosaccharide chains from respiratory mucins.

The total syntheses of several complex oligosaccharide moieties that occur in the core structure of sulfated mucins are reported. A trisaccharide acceptor was obtained through regio- and stereoselective sialylation of methyl (6-O-pivaloyl-beta-D-galactopyanosyl)(1-->3)-4,6-O-benzylidene-2-a cetamido-2-deoxy-alpha-D-galactopyranoside with a novel sialyl donor. A tetrasaccharide, pentasaccharide, and hexasaccharide were constructed in predictable and controlled manner with high regio- and stereoselectivity after the successful preparation and employment of a disaccharide donor, trisaccharide donor, disaccharide acceptor, and trisaccharide acceptor building blocks. Finally, a mild oxidative cleaving method was adopted for the selective removal of 2-naphthylmethyl (NAP) in the presence of benzyl groups.