Cross-metathesis of C-allyl iminosugars with alkenyl oxazolidines as a key step in the synthesis of C-iminoglycosyl alpha-amino acids. A route to iminosugar containing C-glycopeptides

[structures: see text] A general access to a novel class of sugar alpha-amino acids composed of iminofuranose and iminopyranose residues anomerically linked to the glycinyl group through an alkyl chain is described. A set of eight compounds was prepared by the same reaction sequence involving as an initial step the Grubbs Ru-carbene-catalyzed cross-metathesis (CM) of various N-Cbz-protected allyl C-iminoglycosides with N-Boc-vinyl- and N-Boc-allyloxazolidine. The isolated yields of the CM products (mixtures of E- and Z-alkenes) varied in the range 40-70%. Each mixture was elaborated by first reducing the carbon-carbon double bond using in situ generated diimide and then unveiling the N-Boc glycinyl group [CH(BocNH)CO2H] by oxidative cleavage of the oxazolidine ring by the Jones reagent. All amino acids were characterized as their methyl esters. The insertion of a model C-iminoglycosyl-2-aminopentanoic acid into a tripeptide via sequential carboxylic and amino group coupling with L-phenylalanine derivatives was carried out as a demonstration of the potential of these sugar amino acids in designed glycopeptide synthesis.     

Detection of glucosamine in the acid hydrolysis solution of humic substances

Several humic substances isolated from water and soil have been characterized applying acid hydrolysis to release defined components bound in these high molecular organic compounds. The hydrolysis solution have been analyzed by HPLC after precolumn derivatization with o-phthalaldehyde and 9-fluorenylmethylchloroformate. Under these conditions the nitrogen containing carbohydrate glucosamine could be detected and separated besides seventeen amino acids. The results show that 8.0 to 40.1% of the total nitrogen content of the investigated samples contributes to amino acids and up to 7.9% to the carbohydrate glucosamine. It could be deduced that defined amino acid carbohydrate building blocks were bound in humic substances, because the glucosamine nitrogen content correlates with the calculated amino acid nitrogen. Furthermore the total amino acid nitrogen amount of natural organic matter can be estimated from the results of the determination of glucosamine.     

Boronated derivatives of protohemin IX with L-amino acids as potential anticancer agents

New water-soluble conjugates of protohemin IX with an anionic 1-carba-closo-dodecaborate polyhedron and L-amino acids have been synthesized. In these compounds, the amino acid residues are bound to the porphyrin ring through the amide or ester bond. The new water-soluble amino acid derivatives of boronated protohemin IX show high antitumor activity for human tumor cell lines.     

Detection of glucosamine in the acid hydrolysis solution of humic substances

Several humic substances isolated from water and soil have been characterized applying acid hydrolysis to release defined components bound in these high molecular organic compounds. The hydrolysis solution have been analyzed by HPLC after precolumn derivatization with o-phthalaldehyde and 9-fluorenylmethylchloroformate. Under these conditions the nitrogen containing carbohydrate glucosamine could be detected and separated besides seventeen amino acids. The results show that 8.0 to 40.1% of the total nitrogen content of the investigated samples contributes to amino acids and up to 7.9% to the carbohydrate glucosamine. It could be deduced that defined amino acid carbohydrate building blocks were bound in humic substances, because the glucosamine nitrogen content correlates with the calculated amino acid nitrogen. Furthermore the total amino acid nitrogen amount of natural organic matter can be estimated from the results of the determination of glucosamine.     

Synthesis and Evaluation of a Cyclophane Receptor for Acetic Acid

A bicyclic cyclophane ( 2 ) containing one pyridine nitrogen and four amide N-H groups oriented toward the interior of the cavity was synthesized. The binding constants of various carboxylic acids with 2 were measured by UV/Vis spectroscopy. Acetic acid bound to 2 with a K a of 980 - 90 M m 1 in chloroform while branched carboxylic acids showed significantly lower binding. The data indicate that acetic acid was bound within the cavity of 2 . Only one acetic acid binds to two control hosts, whereas 2 shows definitive 1:1 binding. The results suggest that selectivity in the binding of carboxylic acids can be achieved via size constraints dictated by the receptor cavity, and that the same size restrictions lead to only one carboxylic acid bound to the cyclophane. The crystal structure of 2 is reported.     

Ion-pair interaction in pyridinium carboxylate solutions

Ion-pair interactions between pyridinium cations and various carboxylate anions are explored using noisy light based coherent anti-Stokes Raman scattering (I(2)CARS). Binary mixtures of pyridine and various carboxylic acids (including halo-acetic acids, straight-chain carboxylic acids, and pivalic acid) are prepared. A Br?nsted type acid-base reaction occurs in these mixtures to create pyridinium and carboxylate ions. Both pyridine, itself, and pyridinium have strong I(2)CARS signals originating from their ring breathing modes. The vibrational frequency of the ring breathing mode for pyridine is blue-shifted by hydrogen bonding, and that same mode for pyridinium is red-shifted by ion-pair interaction. Frequency shift data for the ring breathing mode of pyridine and pyridinium are presented. These data are discussed in terms of a simplistic model for the electronic behavior of these compounds.     

Reaction intermediates of a dihydropyridine derivative of 2′,3′-dideoxycytidine related to AIDS dementia studied by laser flash photolysis

A derivative of 2′,3′-dideoxycytidine (ddC), carrying one 1,4-dihydro-1-methyl-3-pyridinyl-carbonyl group at the cytidine exocyclic amino group and one at the ribose 5-hydroxyl group, was exposed in water-ethanol solution to high-power pulsed laser emission at a wavelength of 354.7 nm. Measurement of the transient absorption spectra with nanosecond time resolution shows that the photoejection of an electron occurs due to stepwise two-photon absorption by the dihydropyridine via its fluorescent state. The spectrum of the cation radical formed in this reaction was determined, together with that of the neutral radical appearing following deprotonation of the cation. The electron is apparently abstracted only from the pyridine group attached to the ribose, since a comparative study on ddC carrying a dihydropyridine only at the exocyclic amino group showed no evidence for photoionization in the same experimental conditions.     

N‐Benzylnicotinamide and N‐benzyl‐1,4‐dihydronicotinamide: useful models for NAD+ and NADH

3‐Aminocarbonyl‐1‐benzylpyridinium bromide (N‐benzylnicotinamide, BNA), C₁₃H₁₃N₂O⁺·Br⁻, (I), and 1‐benzyl‐1,4‐dihydropyridine‐3‐carboxamide (N‐benzyl‐1,4‐dihydronicotinamide, rBNA), C₁₃H₁₄N₂O, (II), are valuable model compounds used to study the enzymatic cofactors NAD(P)⁺ and NAD(P)H. BNA was crystallized successfully and its structure determined for the first time, while a low‐temperature high‐resolution structure of rBNA was obtained. Together, these structures provide the most detailed view of the reactive portions of NAD(P)⁺ and NAD(P)H. The amide group in BNA is rotated 8.4 (4)° out of the plane of the pyridine ring, while the two rings display a dihedral angle of 70.48 (17)°. In the rBNA structure, the dihydropyridine ring is essentially planar, indicating significant delocalization of the formal double bonds, and the amide group is coplanar with the ring [dihedral angle = 4.35 (9)°]. This rBNA conformation may lower the transition‐state energy of an ene reaction between a substrate double bond and the dihydropyridine ring. The transition state would involve one atom of the double bond binding to the carbon ortho to both the ring N atom and the amide substituent of the dihydropyridine ring, while the other end of the double bond accepts an H atom from the methylene group para to the N atom.     

First asymmetric syntheses of 6-substituted nipecotic acid derivatives

Various nipecotic acid derivatives are known to be potent GABA uptake inhibitors thus being useful in the treatment of a number of neurological and psychological disorders. In this paper, the first asymmetric syntheses of 6-substituted nipecotic acid derivatives are presented. The synthetic strategy was designed to provide access to a large variety of enantiomerically pure 6-substituted nipecotic acid derivatives. The synthesis starts from the chiral N-acyldihydropyridines 15 and 16 obtained via asymmetric electrophilic α-amidoalkylation reaction of a chiral N-acylpyridinium ion. These were utilized for the preparation of enantiomerically pure 6-(4,4-diphenylbutyl)nipecotic acids and 6-(4,4-diphenylbutenyl)nipecotic acids in a multistep synthesis, including the removal of the dimethylphenylsilyl blocking group from the dihydropyridine ring, the reduction of the dihydropyridine heterocycle, a Horner-Wittig reaction and the removal of the chiral auxiliary. The obtained target molecules, however, showed only negligible affinity to the GAT-1- and GAT-3 transport proteins.     

A novel synthesis of N-methyl asparagine,arginine, histidine,and tryptophan

[reaction: see text] N-Methyl amino acid residues in peptides modify several pharmacologically useful parameters, but synthesis of alkylated peptides is hampered by unavailability of N-methylated monomers. The syntheses of four N-methyl amino acids with basic side chains are presented. The side chains of these basic amino acids needed to be specially protected or constructed. This completes the set of 20 common L-amino acid N-methyl derivatives prepared via 5-oxazolidinone intermediates by our group.     

Photosensitized oxidation of unsymmetrical 1,4-dihydropyridines

Photosensitized oxidation of unsymmetrically substituted 1,4-dihydropyridines using dye sensitizers methylene blue, rose bengal and tetraphenylporphyrin by taking visible light source resulted in the aromatization of dihydropyridine ring and formation of the corresponding pyridine derivatives. Comparison of the results obtained under photosensitized reaction with those obtained by direct photo-oxidation indicated a very fast and smooth reaction of these compounds and formation of pyridine derivatives using theses dyestuffs.     

Synthesis of Novel Pyran β-Amino Acid and 5,6-Dihydro-2H-pyran β-aminoxy Acid from Carbohydrate Derivatives

Synthesis of two new amino acids, containing pyran rings, is reported from carbohydrate derivatives. The cis-3-amino-pyran-2-carboxylic acid (cis-APyC) was prepared from (R)-glyceraldehyde derivative, using nucleophilic substitution reaction for pyran ring formation. Similarly, the trans-3-aminoxy-5,6-dihydro-2H-pyran-2-carboxylic acid (trans-AmPyC) was prepared from diacetone glucose (DAG), using ring closing metathesis (RCM) reaction for the ring formation.     

Two 1,4‐dihydropyridine derivatives with potential calcium‐channel antagonist activity

The title compounds, benzyl 4‐(3‐chloro‐2‐fluorophenyl)‐2‐methyl‐5‐oxo‐4,5,6,7‐tetrahydro‐1H‐cyclopenta[b]pyridine‐3‐carboxylate, C₂₃H₁₉ClFNO₃, (I), and 3‐pyridylmethyl 4‐[2‐fluoro‐3‐(trifluoromethyl)phenyl]‐2,6,6‐trimethyl‐5‐oxo‐1,4,5,6,7,8‐hexahydroquinoline‐3‐carboxylate, C₂₆H₂₄F₄N₂O₃, (II), belong to a class of 1,4‐dihydropyridines whose members sometimes display calcium modulatory properties. The 1,4‐dihydropyridine ring in each structure has a shallower than usual shallow‐boat conformation and is nearly planar in (I). In each structure, the halogen‐substituted benzene ring is oriented such that the halogen substituents are in a synperiplanar orientation with respect to the 1,4‐dihydropyridine ring plane. The oxocyclopentene ring in (I) is planar, while the oxocyclohexene ring in (II) has a half‐chair conformation, which is less commonly observed than the envelope conformation usually found in related compounds. In (I), the frequently observed intermolecular N—H...O hydrogen bond between the amine group and the carbonyl O atom of the oxocyclopentene ring of a neighbouring molecule links the molecules into extended chains; there are no other significant intermolecular interactions. By contrast, the amine group in (II) forms an N—H...N hydrogen bond with the pyridine ring N atom of a neighbouring molecule. Additional C—H...O interactions complete a two‐dimensional hydrogen‐bonded network. The halogen‐substituted benzene ring has a weak intramolecular π–π interaction with the pyridine ring. A stronger π–π interaction occurs between the 1,4‐dihydropyridine rings of centrosymmetrically related molecules.     

Design, synthesis and biological evaluation of thrombin inhibitors based on a pyridine scaffold

A series of 2,4-disubstituted pyridine derivatives has been designed, synthesised and evaluated as thrombin inhibitors. A Grignard exchange reaction was used to introduce various benzoyl substituents in position 4 of the pyridine ring, where they serve as P3 residues in binding to thrombin. In position 2 of the pyridine ring, a para-amidinobenzylamine moiety was incorporated as P1 residue by an SNAr reaction using ammonia as nucleophile followed by a reductive amination. A crystal structure obtained for one of the compounds in the active site of thrombin revealed that the basic amidine group of the inhibitor was anchored to Asp 189 at the bottom of the S1 pocket. A comparison with melagatran, bound in the active site of thrombin, revealed a good shape match but lack of hydrogen bonding possibilities in the S2-S3 region for the thrombin inhibitors reported in this study.     

A compilation of amino acid analyses of proteins

The amino acid analyses of 186 proteins are given as residues per 1000 residues. Additional information as carbohydrate composition, content of uncomon amino acids, and sources of all proteins are also presented.     

Kinetics and mechanism of transaldimination of amino acids and aromatic amines with pyridoxal

Kinetics and mechanism of transaldimination of amino acids and aromatic amines with pyridoxal have been studied by means of UV spectroscopy and polarimetry. It has been shown that aminal intermediates are formed in reaction of the Schiff’s bases with p-aminobenzoic acid and β-alanine. The structure of aminal and Schiff’s base is determined by the spatial arrangement of the amino acid and aromatic fragments with respect to the pyridine ring plane. The presence of OH and CH₂-OH groups in the o-positions in pyridoxal structure turns amino groups by 90° with respect to the pyridine ring. The scheme of Schiff’s bases transaldimination by amino acids and biological amines has been developed according to stereospecific, energy, and geometric factors.     

Synthesis of 1-hydroxy-substituted pyrazolo[3,4-c]- and pyrazolo[4, 3-c]quinolines and -isoquinolines from 4- and 5-aryl-substituted 1-benzyloxypyrazoles

1-Hydroxypyrazolo[3,4-c]quinoline (22), 1-hydroxypyrazolo[4, 3-c]quinoline (21), 1-hydroxypyrazolo[3,4-c]isoquinoline (20), and 1-hydroxypyrazolo[4,3-c]isoquinoline (19) were prepared from 1-benzyloxypyrazole (6), establishing the pyridine B-ring in the terminal step. The pyridine ring of pyrazoloquinolines 14 and 18 was formed via cyclization of a formyl group at C-4 or C-5 and an amino group of a 2-aminophenyl substituent at C-5 or C-4 in 1-benzyloxypyrazole. The pyridine ring of pyrazoloisoquinolines 5 and 9 was created via cyclization of a formyl group in a 2-formylphenyl substituent at C-4 or C-5 with an iminophosphorane group installed at C-5 or C-4 of 1-benzyloxypyrazole by lithiation followed by reaction with tosyl azide and then with tributylphoshine utilizing the Staudinger/aza-Wittig protocol. The 2-aminophenyl and the 2-formylphenyl substituent were introduced at C-5 or C-4 by regioselective metalation followed by transmetalation to the pyrazolylzinc halide and subsequent palladium-catalyzed cross-coupling with 2-iodoaniline or 2-bromobenzaldehyde. The order of reactions and use of protecting groups in the individual sequences have been optimized. The 1-benzyloxy-substituted pyrazoloquinolines and isoquinolines thus obtained were debenzylated by strong acid to the corresponding 1-hydroxy-substituted pyrazoloquinolines and isoquinolines 19-22.     

Interactions of cyclodextrins with aromatic amino acids: a basis for protein interactions

Cyclodextrins (CyD) have proven effects on the stability of proteins and can be used in the formulation of aggregation prone therapeutic proteins. This effect stems from specific interactions between the CyD (preferably β-CyD) and solvent exposed amino acid residues. Here the interaction with hydrophobic aromatic amino acid residues stands out and the interaction between CyDs and these amino acid residues holds the key to understanding the observed effects, which CyDs exerts on proteins and peptides. Here we present a comparative study of the interactions between free and peptide bound aromatic amino acids and their derivatives with α, β and γ-CyDs using NMR spectroscopy. We propose a novel, quantitative means of assessing the penetration depth of guest molecules in CyD cavities, the penetration gauge Π, and apply it to the observed interaction patterns from ROESY NMR spectra. We demonstrate that the penetration depths of the aromatic rings within the CyDs rely highly on the nature of the remainder of the guest molecule. Thus the presence of charges, neighboring amino acids and the specific positioning on the surface of a protein highly influences the penetration depth and geometry of guest–CyD interactions.     

A compilation of amino acid analyses of proteins

The amino acid analyses of 183 proteins, as residues per 1000 residues, are given. In addition the carbohydrate content and the content of any noncommon amino acids are also given. The sources of all proteins are presented.     

Comparison of the performance of immunosorbents prepared by site-directed or random coupling of monoclonal antibodies.

The majority of methods used to prepare immunosorbents immobilize antibodies through their reactive amino acid residues. The bound antibody activity of these immunosorbents is low. Hydrazide-based matrices couple antibodies through carbohydrate chains frequently located in the Fc region. This paper reports a comparative study of the performance of immunosorbents prepared by cyanogen bromide or hydrazide immobilization methods. The experiments utilized murine monoclonal antibodies to the human plasma proteins Factor IX or Protein C. The antibodies were immobilized at low densities to beaded agarose matrices which had similar properties. The hydrazide immunosorbents had binding efficiencies which were lower (anti-Factor IX) or up to 1.6-fold higher (anti-Protein C) than comparable cyanogen bromide coupled gels. However, there was no improvement in performance due to lower recoveries of bound protein from the hydrazide gels. Control experiments demonstrated that oxidation of antibody which is required for its coupling to hydrazide gels had no effect on antibody binding to antigen. Our results indicate that, as with cyanogen bromide coupling methods, site-directed immobilization through carbohydrate residues results in a restricted ability to bind to antigen. Both monoclonals were found to contain carbohydrate in their Fab' regions through which coupling may have occurred. The frequency of carbohydrate in the Fab region and the ability to control glycosylation at these sites are factors which may impact the utility of carbohydrate-directed immobilization of antibodies.