One-bead, one-compound peptide library sequencing via high-pressure ammonia cleavage coupled to nanomanipulation/nanoelectrospray ionization mass spectrometry

Biological screening of one-bead, one-compound (OBOC) combinatorial peptide libraries is routinely carried out with the peptide remaining bound to the resin bead during screening. After a hit is identified, the bead is isolated, the peptide is cleaved from the bead, and its sequence is determined. We have developed a new technique for cleavage of peptides from resin beads whereby exposure of a 4-hydroxymethyl benzoic acid (HMBA)-linked peptide to high-pressure ammonia gas led to efficient cleavage in as little as 5 min. Here we also report a new method of extracting peptide from individual library beads for its introduction into a mass spectrometer that uses nanomanipulation combined with nanoelectrospray ionization mass spectrometry (NSI MS). Single beads analyzed by nanomanipulation/NSI MS were found to give identical MS results to those of bulk samples. Detection of 18 unique cleaved peptides 1 to 8 amino acids in length, and sequencing of 14 different peptide sequences 4 to 8 amino acids in length, was demonstrated on a combination of bulk samples and ones from individual beads of an OBOC library. The method was highly reproducible, with 100% of attempts to extract peptide resulting in high-quality MS data. This new collection of techniques allows rapid, reliable, environmentally responsible sequencing of hit beads from combinatorial peptide libraries.     

Novel azido fatty acid ester derivatives from conjugated C(18) enynoate.

Methyl octadec-11Z-en-9-ynoate (1) was epoxidized to give methyl 11,12-Z-epoxy-octadec-9-ynoate (2, 81%). Acid catalyzed ring opening of the epoxy ring of compound 2 gave methyl 11,12-dihydroxy-octadec-9-ynoate (3, 80%). The latter was treated with mesyl chloride to yield methyl 11,12-dimesyloxy-octadec-9-ynoate (4, 76%). Reaction of compound 4 with sodium azide furnished methyl 11-azido-12-mesyloxy-octadec-9-ynoate (5a, 49%) and methyl 11-azido-octadec-11E-en-9-ynoate (5b, 24%). Compound 2 was semi-hydrogenated over Lindlar catalyst to give methyl 11,12-Z-epoxy-octadec-9Z-enoate (6, 90%). This allylic epoxy fatty ester (6) was reacted with sodium azide to give a mixture of methyl 11-azido-12-hydroxy-octadec-9Z-enoate (7a) and methyl 9-azido-12-hydroxy-octadec-9E-enoate (7b), which could not be separated into individual components by silica chromatography. Chromic acid oxidation of the mixture of compounds 7a and 7b furnished methyl 9-azido-12-oxo-octadec-10E-enoate (8, 42% based on amount of compound 6 used) and an intractable mixture of polar compounds. The various products were characterized by NMR spectroscopic and mass spectral analyses.     

Synthesis of 3-methylpseudouridine and 2′-deoxy-3-methyl-pseudouridine

The first chemical synthesis of 3-methyl-ψ-uridine (5) and its 2′-deoxy analogue (9) has been achieved. ψ-Uridine was trimethylsilylated and the crude product was treated with acetyl chloride, to give the 1-acetyl derivative (3). Crude 3 was methylated with dimethoxymethyldimethylamine and then saponified, to give crystalline 5 in 82% overall yield. Treatment of 5 with 1,3-dichloro-1,1,3,3-tetraiso-propyldisiloxane afforded the 3′,5′-protected product, which was converted into the 2′-O-[(imidazol-1-yl)thiocarbonyl] derivative 7. Reduction of 7 with tributyltin hydride followed by deblocking of the product gave crystalline 2′-deoxy-3-methyl-ψ-uridine (9) in 35% yield from 5.     

Solid-phase synthesis of 4-substituted imidazoles using a scaffold approach

Immobilized 4-iodoimidazole 2 was used in a metal/halogen exchange reaction followed by treatment with electrophiles and subsequent cleavage from the resin to yield 4-substituted imidazoles 8-11. Grignard reaction with the resin-bound ketones 5 yielded the corresponding alcohols 11. This approach was used for a library synthesis of 35 imidazoles.     

Repeating structure of chick tropoelastin revealed by complementary DNA cloning

A cDNA library was constructed from chick aorta poly(adenylic acid)-containing RNA in the expression vector pEX1. Several clones were identified by screening the library with a polyclonal antiserum raised against chick tropoelastin and confirmed by DNA sequencing. Analysis of the deduced amino acid sequence, corresponding to the mature tropoelastin and most of the signal peptide, revealed that the molecule is composed of at least 8, and possibly 13, repeating units. The common features of each unit include an N-terminal region composed largely of alanines and lysines and ending with an aromatic amino acid, followed by a GAG span and then a C-terminal region consisting mostly of valines, prolines, and glycines often present in several copies of the sequence (VPGV). This structure is discussed in terms of the functional properties of the molecule.     

7-substituted 8-aza-7-deazapurines and 2,8-diaza-7-deaza-purines: synthesis of nucleosides and oligonucleotides

7-Substituted 8-aza- 7-deazaadenosines 1a-e were synthesized by Sonogashira cross coupling from the corresponding 7-iodo nucleoside in 36-79% yields. Starting from 7-bromo (or 7-iodo)-8-aza-7-deazaadenine, 2a,b were obtained by acid-catalyzed glycosylation followed by deprotection in 53 and 35% yields, repectively. Compounds 2b was applied to cross coupling reaction to give 2c-d in 34-95% yield. Compounds 2a and 4b were further transformed to the phosphoramidites 5 and 6b in 9 and 49% overall yields, which were incorporated into oligonucleotides.     

Novel inhibitors of an emerging target in Mycobacterium tuberculosis; substituted thiazolidinones as inhibitors of dTDP-rhamnose synthesis

The emergence of multi-drug resistant tuberculosis, coupled with the increasing overlap of the AIDS and tuberculosis pandemics has brought tuberculosis to the forefront as a major worldwide health concern. In an attempt to find new inhibitors of the enzymes in the essential rhamnose biosynthetic pathway, a virtual library of 2,3,5 trisubstituted-4-thiazolidinones was created. These compounds were then docked into the active site cavity of 6'hydroxyl; dTDP-6-deoxy-D-xylo-4-hexulose 3,5-epimerase (RmlC) from Mycobacterium tuberculosis. The resulting docked conformations were consensus scored and the top 5% were slated for synthesis. Thus far, 94 compounds have been successfully synthesized and initially tested. Of those, 30 (32%) have > or =50% inhibitory activity (at 20 microM) in the coupled rhamnose synthetic assay with seven of the 30 also having modest activity against whole-cell M. tuberculosis.     

Identification of putative parasitism genes expressed in the esophageal gland cells of the soybean cyst nematode Heterodera glycines

Cloning parasitism genes encoding secretory proteins expressed in the esophageal gland cells is the key to understanding the molecular basis of nematode parasitism of plants. Suppression subtractive hybridization (SSH) with the microaspirated contents from Heterodera glycines esophageal gland cells and intestinal region was used to isolate genes expressed preferentially in the gland cells of parasitic stages. Twenty-three unique cDNA sequences from a SSH cDNA library were identified and hybridized to the genomic DNA of H. glycines in Southern blots. Full-length cDNAs of 21 clones were obtained by screening a gland-cell long-distance polymerase chain reaction cDNA library. Deduced proteins of 10 clones were preceded by a signal peptide for secretion, and PSORT II computer analysis predicted eight proteins as extracellular, one as nuclear, and one as plasmalemma localized. In situ hybridization showed that four of the predicted extracellular clones were expressed specifically in the dorsal gland cell, one in the subventral gland cells, and three in the intestine in H. glycines. The predicted nuclear clone and the plasmalemma-localized clone were expressed in the subventral gland cells and the dorsal gland cell, respectively. SSH is an efficient method for cloning putative parasitism genes encoding esophageal gland cell secretory proteins that may have a role in H. glycines parasitism of soybean.     

7-SUBSTITUTED 8-AZA-7-DEAZAPURINES AND 2,8-DIAZA-7-DEAZA-PURINES: SYNTHESIS OF NUCLEOSIDES AND OLIGONUCLEOTIDES

7-Substituted 8-aza-7-deazaadenosines 1a–e were synthesized by Sonogashira cross coupling from the corresponding 7-iodo nucleoside in 36–79% yields. Starting from 7-bromo (or 7-iodo)-8-aza-7-deazaadenine, 2a,b were obtained by acid-catalyzed glycosylation followed by deprotection in 53 and 35% yields, repectively. Compounds 2b was applied to cross coupling reaction to give 2c-d in 34–95% yield. Compounds 2a and 4b were further transformed to the phosphoramidites 5 and 6b in 9 and 49% overall yields, which were incorporated into oligonucleotides.     

Parallel solid-phase synthesis of a model library of 7alpha-alkylamide estradiol derivatives as potential estrogen receptor antagonists.

The C17-THP derivative of 7alpha-(11-azidoundecanyl)-estradiol (4) was synthesized and coupled to an aminomethyl resin via a photolabile o-nitrobenzyl linker. Reduction of the azide by the Staudinger reaction to its corresponding amine followed by acylation using four activated NFmoc protected amino acids gave a first level of diversity. Subsequent deprotection of the Fmoc followed by a second acylation with five activated carboxylic acids produced, after photocleavage, a model library of twenty antiestrogen-related 7alpha-alkylamide estradiol derivatives in acceptable overall yields and very good purities.     

Assembly of the membrane attack complex of complement on small unilamellar phospholipid vesicles

Light-scattering intensity was shown to be a reliable, direct, and quantitative technique for monitoring the assembly of the membrane attack complex of complement (proteins C5b-6, C7, C8, and C9) on small unilamellar phosphatidylcholine vesicles. The assembly on vesicles occurred in a simple fashion; complexes of C5b-7 bound noncooperatively to the vesicles, and final assembly of C5b-9 did not induce vesicle aggregation or fragmentation. When C5b-6 and C7 were mixed in the presence of vesicles but at molar protein/vesicle ratios of less than 1, there was quantitative binding of C5b-7 to the vesicles with no concomitant aggregation of C5b-7. If C7 was added at a slower rate, quantitative binding was obtained at molar C5b-7/vesicle ratios of up to 5. The latter observations (a) were consistent with the proposal that C5b-7 aggregation and membrane binding were competitive events and (b) defined conditions under which light-scattering intensity measurements could monitor C5b-9 assembly on vesicles without contribution from the fluid-phase assembly. The C8/C5b-7 ratio in the phospholipid-C5b-8 complex was 0.97 +/- 0.12, and the maximum ratio of C9/C5b-8 in the final complex was 16.2 +/- 2.0. One C9 molecule associated rapidly with each phospholipid-C5b-8, followed by slower incorporation of the remaining C9 molecules. The initial velocity of the slow phase of C9 addition was easily saturated with C9 and gave an activation energy of 37 kcal/mol. This was identical with the value measured for the analogous process in the fluid-phase assembly.(ABSTRACT TRUNCATED AT 250 WORDS)     

Synthesis of beta-D-GlcA-(1----3)-beta-D-Gal disaccharides with 4- and 6-sulfate groups and 4,6-disulfate groups.

The sodium salts of the 6-sulfate 7, the 4-sulfate 10, and the 4,6-disulfate 12 of benzyl 3-O-(beta-D-glucopyranosyl uronate)-beta-D-galactopyranoside (5) have been synthesized. Methyl (2,3,4-tri-O-acetyl-1-bromo-1-deoxy-alpha-d-glucopyran)uronate (1) was coupled with benzyl 2-O-benzoyl-4,6-O-benzylidene-beta-D-galactopyranoside (2) to yield 3. The benzylidene acetal of 3 was hydrolyzed to give benzyl 2-O-benzoyl-3-O-[methyl (2,3,4-tri-O-acetyl-beta-D-glucopyranosyl)uronate]-beta-D-galactopyra noside (4). Compound 4 was utilized as a key intermediate to prepare the sulfated disaccharides 7,10, and 12. Direct sulfation of 4 with sulfur trioxide-trimethylamine for 2 days yielded the 6-sulfate 6. The 4,6-disulfate 11 was accessible by running the reaction under the same conditions for 14 days. The 4-sulfate 9 was obtained after protecting the 6-OH group of 4 by reaction with benzoyl imidazole to give the 6-benzoate 8, followed by sulfation under vigorous conditions. Treatment of the protected compounds 4, 6, 9, and 11 with aqueous sodium hydroxide in tetrahydrofuran gave the unprotected 5, 7, 10, and 12, respectively.     

Method for the synthesis of uric acid derivatives

A general procedure to obtain tetra-substituted uric acid by stepwise N-alkylation is described. 2,6-Dichloropurine (1) was condensed with 1-propanol by Mitsunobu reaction to give 9-propyl congener (2). Treatment of 2 with ammonia gave adenine derivative (4a), which was converted to the 8-oxoadenine (5b) in 3 steps. Methylation of 5b proceeded site-specifically to give 6-amino-2-chloro-7,8-dihydro-7-methyl-9-propylpurin-8-one (6) as a sole product. Compound 6 was successively treated with NaNO2 and iodomethane to give 2-chloro-1,6,7,8-tetrahydro-1,7-dimethyl-9-propylpurin-6,8-dione (9) accompanied by the O6-methyl product (8) in 75% and 6.9%, respectively. After nucleophilic substitution of 9 with NaOAc, the product (11) was reacted with iodomethane to give the uric acid (12) and the 2-methoxy product (13) in 46% and 15.5%, respectively. However, the reaction of 11 with the benzylating agents gave only O-benzyl products (14a,b).     

Resistance to Aphis glycines (Hemiptera: Aphididae) in various soybean lines under controlled laboratory conditions

The soybean aphid, Aphis glycines Matsumura (Hemiptera: Aphididae), a pest of soybean, Glycine max (L.) Merr., native to Asia, has recently become a principal pest of this crop in many areas of North America. Insecticides are currently used to manage A. glycines, but host plant resistance is a potential alternative management tool. Tests were conducted to determine resistance to A. glycines among soybean lines. 'Cobb,' 'Tie-feng 8,' and 'Jackson' were resistant to population growth of A. glycines compared with 'Cook' and '91B91,' a susceptible control. Antibiosis was evident in Cobb, Jackson, and Tie-feng 8 from lowered survival of first generation A. glycines, and in Cobb, Jackson, Tie-feng 8, and 'Braxton' from diminished reproduction by first generation aphids. Antixenosis was apparent in Cobb and Jackson during initial infestation of aphid population growth tests, because A. glycines were unsettled and dispersed readily from placement points on unifoliolate leaves. Decreased nymphiposition by A. glycines occurred on Cobb and Jackson, and it may have been caused by antibiotic chemicals in these lines, failure of aphids to settle, or both. Differences in distribution of A. glycines between unifoliolate leaves and other shoot structures suggest that unifoliolate leaves were acceptable feeding sites on 91B91 and Cook, whereas unifoliolate leaves and other shoot structures were roughly equally acceptable feeding sites on Braxton, Tie-feng 8, Jackson, and Cobb. However, Jackson and Cobb had relatively low counts of A. glycines on shoots that may have been due to abandonment of plants by aphids, decreased aphid survival, or both. Results confirm earlier findings that Jackson is a strong source of resistance to A. glycines, and they suggest that Tie-feng 8, Braxton, and especially Cobb are potentially useful sources of resistance.     

Identification of bacterial clones encoding bovine caseins by direct immunological screening of the cDNA library

A sensitive immunoassay was used to identify recombinant plasmids carrying cDNA fragments of bovine caseins in the cDNA library from bovine mammary gland mRNA. Colonies grown on nitrocellulose filters were lysed in situ and proteins from the lysates were blotted onto CNBr-activated cellulose filter paper. Antigens covalently bound to CNBr-activated paper or bound to nitrocellulose filters were detected by reaction with antiserum to caseins, followed by ¹²⁵I-labelled Staphylococcus aureus protein A and autoradiography. Six clones were found positive among 5400 of the cDNA library: 3-A1, 3-B2, 3-B5, 3-H7, 2-A5 and 2-C9. The molecular weights of chimeric pre-β-lactamase: casein proteins synthesized in Escherichia coli were estimated by immunoblotting. Colony hybridization and nucleotide sequence analysis showed that clone 3-B5 contained a cDNA fragment of bovine χ-casein, clone 3-H7 contained a cDNA fragment of β-casein, while clones 2-A5 and 2-C9 carried cDNA fragments of α_si-casein.     

Hoogsteen vs. Watson-Crick base pairing: incorporation of 2-substituted adenine- and 7-deazaadenine 2'-deoxy-beta-D-ribonucleosides into oligonucleotides

Various 2-substituted 2'-deoxyadenosines and 7-deazaadenosines have been synthesized. The phosphonate building block 9 of 2-chloro-7-deaza-2'-deoxyadenosine (7-deazacladribine; 2) was prepared by 4,4'-dimethoxytritylation of the parent nucleoside (-->7), followed by protection of the amino function with a formamidine residue (-->8). The latter was reacted with PCl3/N-methylmorpholine/1,2,4-triazole to give compound 9. Moreover, 2-methoxy-2'-deoxyadenosine (2'-deoxyspongosine; 1b) was converted into the fully protected derivative 12, which was then transformed into the 2-cyanoethyl phosphoramidite 14. Also the 2-(trifluoromethyl)-substituted 2'-deoxyadenosines 19-21 were prepared by glycosylation of the chromophore 16 with the halogenose 17, followed by one-pot deprotection and nucleophilic displacement of the 6-Cl substituent. The new DNA building blocks 9 and 14 were used--together with formerly prepared cladribine derivative 4--for solid-phase synthesis of a series of oligodeoxyribonucleotides. These were studied with respect to their thermal stability as well as of the base pairing mode (Watson-Crick vs. Hoogsteen) of modified bases.     

Fluid-phase assembly of the membrane attack complex of complement

The dynamics and protein stoichiometry of the fluid-phase assembly of the membrane attack complex of complement were characterized by using light-scattering intensity measurements. The assembly proceeded in an ordered manner with generation of stable and highly reproducible intermediates. In the absence of phospholipid or C8, mixtures of C5b-6 and C7 self-associated to fluid phase-C5b-7 which had a weight-average molecular weight of (4.1 +/- 0.2) X 10(6). This corresponded to an average of nine C5b-7 complexes per particle. The particles appeared heterodisperse on sucrose gradients with S20,W values ranging from 21 to 39 S. Addition of C8 and C9 caused no further aggregation or disassembly of the particles. When excess C8 was added to the aggregated C5b-7, the ratio of C8 incorporated per C5b-7 moiety was 0.98 +/- 0.03. At saturating levels of C9, the C9/C5b-8 ratio in the particles was 7.2 +/- 0.6. Incorporation of C8 caused a small increase in the Z-averaged particle diffusion coefficient [(9.9-10.3) X 10(-8) cm2/s], indicating that it added in a manner that "filled in the gaps" in the C5b-7 particles. C9 caused only small decreases in the particle diffusion coefficient and substantially decreased the f/fmin ratio. The time course for C9 incorporation into fluid phase-C5b-8 indicated an initial rapid phase followed by a slow phase. The rapid phase corresponded to the incorporation of about one C9 for every two C5b-8 complexes. This suggested that one C9 binding site was accessible on about half of the C5b-8 complexes. This may imply that only about half of the C5b-8 complexes were capable of C9 polymerization so that the ratio of C9 incorporated per functional C5b-8 was (14 +/- 2)/1. The initial velocity of the slow phase of C9 addition gave an activation energy of 37 kcal/mol. The activation energy for C5b-8-independent polymerization of C9 had a similar value of 41 kcal/mol. Light-scattering intensity measurements seemed to be a highly reliable method for quantitative characterization of the fluid-phase assembly.