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PubMed2005

Dynamic kinetic resolution of amino acid amide catalyzed by D-aminopeptidase and alpha-amino-epsilon-caprolactam racemase.

Amino acid amide racemizing activity was discovered in alpha-amino-epsilon-caprolactam (ACL) racemase (EC 5. 1. 1. 15) from Achromobacter obae. The enzymatic synthesis of d-alanine from l-alanine amide has been demonstrated by use of d-aminopeptidase (DAP; EC 3. 4. 11. 19) from Ochrobactrum anthropi C1-38 and ACL racemase. The conversion of 45 mM l-alanine amide was carried out at 30 degrees C for 7 h; l-alanine amide was completely converted to d-alanine, and no l-alanine was detected. The result of successive enzymatic reaction shows that the combination of ACL racemase and DAP can be applied for dynamic kinetic resolution of dl-amino acid amides to yield d-amino acids.

Achromobacter↗
PubMed2006

Electronic control of amide cis-trans isomerism via the aromatic-prolyl interaction.

The cis-trans isomerization of prolyl amide bonds results in large structural and functional changes in proteins and is a rate-determining step in protein folding. We describe a novel electronic strategy to control cis-trans isomerization, based on the demonstration that interactions between aromatic residues and proline are tunable by aromatic electronics. A series of peptides of sequence TXPN, X = Trp, pyridylalanine, pentafluorophenylalanine, or 4-Z-phenylalanine derivatives (Z = electron-donating, electron-withdrawing, or electron-neutral substituents), was synthesized and Ktrans/cis analyzed by NMR. Electron-rich aromatic residues stabilized cis amide bond formation, while electron-poor aromatics relatively favored trans amide bond formation. A Hammett correlation between aromatic electronics and cis-trans isomerization was observed. These results indicate that the interaction between aromatic residues and proline, which is observed to stabilize cis amide bonds and is also a general stabilizing interaction ubiquitous in proteins and protein-protein complexes, is not stabilized exclusively by a classical hydrophobic effect. To a large extent, the aromatic-prolyl interaction is driven and controllable by an electronic effect between the aromatic ring pi-electrons and the proline ring, consistent with a C-H-pi interaction as the key stabilizing force. The aromatic-prolyl interaction is electronically tunable by 0.9 kcal/mol and is enthalpic in nature. In addition, by combining aromatic ring electronics and stereoelectronic effects using 4-fluoroprolines, we demonstrate broad tuning (2.0 kcal/mol) of cis-trans isomerism in tetrapeptides. We demonstrate a simple tetrapeptide, TWflpN, that exhibits 60% cis amide bond and adopts a type VIa1 beta-turn conformation.

Amides↗
PubMed2006

Hydrogen-bond-directed highly stereoselective synthesis of Z-enamides via Pd-catalyzed oxidative amidation of conjugated olefins.

An efficient procedure for the preparation of Z-enamides has been developed, involving the reaction of primary amides with conjugated olefins using a Pd/Cu cocatalyst system. It was found that certain additives, such as phosphine oxides and phosphonates, increase the efficiency of the reaction in nonpolar solvents under an oxygen atmosphere, thus producing a variety of Z-enamides in high yields with excellent stereoselectivity under Wacker-type conditions. The oxidative amidation reaction has a broad substrate scope, allowing alkyl, aryl, and vinyl amides to react with olefins conjugated with ester, amide, phosphonate, and ketone groups. The notable preference for the formation of Z-enamides is presumably due to the presence of an intramolecular hydrogen bond between the amido proton and the carbonyl oxygen. The energy difference between two plausible sigma-alkylamidopalladium intermediates, leading to Z- and E-isomeric enamide products, respectively, was calculated to be 4.18 kcal/mol. The beta-hydride elimination step is assumed to be a stereochemistry-determining step in the overall oxidative amidation process, with the energy level for the transition state leading to the Z-enamide being 5.35 kcal/mol lower than that leading to the E-isomer. The efficiency of photoisomerization between Z- and E-enamides was observed to be largely dependent on the substrates' substituents, and certain E-enamides could be obtained in synthetically useful yields by photoirradiation of Z-isomers. Synthetic application of the present method was successfully demonstrated by a direct formal synthesis of cis-CJ-15,801.

Alkenes↗
PubMed2006

Synthesis of tertiary beta-hydroxy amides by enolate additions to acylsilanes.

The synthesis of tertiary beta-hydroxy amides from acylsilanes, acetamides, and electrophiles is described. The addition of amide enolates to acylsilanes generates beta-silyloxy homoenolate reactivity by undergoing a 1,2-Brook rearrangement. These unique nucleophiles formed in situ can then undergo smooth addition to alkyl halides, aldehydes, and ketones. Enolates derived from amides are crucial for the success of this process since ketone enolates suffer from internal return of the beta-carbanion onto the carbonyl carbon. The use of optically active amide enolates delivers beta-hydroxy amide products with good levels of diastereoselectivity (>/=10:1).

Acylation↗
PubMed1999

Hydrolysis of naptalam and structurally related amides: inhibition by dissolved metal ions and metal (hydr)oxide surfaces.

In metal ion-free solutions, the secondary amide naptalam hydrolyzes more rapidly as the pH is decreased; intramolecular nucleophilic attack by a carboxylate side group is very likely involved. Millimolar levels of dissolved Cu(II) and Zn(II) inhibit hydrolysis between pH 3.6 and pH 6.5. Metal ion-naptalam complex formation is important since addition of the competitive ligand citrate lessens the inhibitory effect. The metal (hydr)oxide surfaces Al(2)O(3) and FeOOH inhibit naptalam hydrolysis to a lesser degree; inhibition is proportional to the extent of naptalam adsorbed. Secondary amides (propanil, salicylanilide, and N-1-naphthylacetamide) and tertiary amides (N-methyl-N-1-naphthylacetamide, furalaxyl, and N, N-diethylsalicylamide) that lack carboxylate side groups do not hydrolyze within 45 days of reaction, even when millimolar Cu(II) concentrations are present. Tertiary amides possessing carboxylate side groups (N,N-diethyl-3,6-difluorophthalamic acid and N, N-dimethylsuccinamic acid) do hydrolyze but are insensitive to the presence or absence of Cu(II). The inhibitory effect is believed to occur via metal coordination of (1) the carbonyl group of naptalam, which induces deprotonation of the amide group and makes the substrate less reactive toward nucleophilic attack; (2) the free carboxylate group of naptalam, which blocks intramolecular nucleophilic attack; or (3) a combination of the two.

Agrochemicals↗
PubMed1991

Synthesis and copper-dependent antimycoplasmal activity of amides and amidines derived from 2-amino-1,10-phenanthroline.

A series of both aliphatic and aromatic amides and aromatic amidines derived from 2-amino-1,10-phenanthroline (3) according to the Topliss scheme were synthesized and subsequently tested for antimycoplasmal potency. Although the compounds themselves showed no activity, in the presence of a nontoxic copper concentration of 40 microM all compounds appeared to be very active against Mycoplasma gallisepticum K154. The most active compounds were found in the amide series and show growth inhibition in the nanomolar range. These compounds are 4 times more active than tylosin, a macrolide antibiotic, which is used therapeutically in veterinary practice. In the presence of copper, amides derived from 3 are more active than corresponding amidines. Increased activity following derivatization of 3 may be due to the presence of a third coordination site for copper in the title compounds. Evaluation of biological data revealed that antimycoplasmal activity of amides derived from 3 is dependent on lipophilicity. For these amides a good linear correlation was found between antimycoplasmal activity and hydrophobic fragmental values for substituents considered. This quantitative structure-activity relationship study indicated that antimycoplasmal activity was increased upon a decrease of these hydrophobic fragmental values.

Amides↗
PubMed1988

Retinobenzoic acids. 1. Structure-activity relationships of aromatic amides with retinoidal activity.

Two types of aromatic amides, terephthalic monoanilides and (arylcarboxamido)benzoic acids, have been shown to possess potent retinoidal activities and can be classified as retinoids. The structure-activity relationships of these amides are discussed on the basis of differentiation-inducing activity on human promyelocytic leukemia cells HL-60. In generic formula 4 (X = NHCO or CONH), the necessary factors to elicit the retinoidal activities are a medium-sized alkyl group (isopropyl, tert-butyl, etc.) at the meta position and a carboxyl group at the para position of the other benzene ring. The bonding of the amide structure can be reversed, this moiety apparently having the role of locating the two benzene rings at suitable positions with respect to each other. Substitution at the ring position ortho to the amide group or N-methylation of the amide group caused loss of activity, presumably owing to the resultant change of conformation. It is clear that the mutual orientation of the benzylic methyl group(s) and the carboxyl group and their distance apart are essential factors determining the retinoidal activity. Among the synthesized compounds, 4-[(5,6,7,8-tetrahydro-5,5,8,8-tetramethyl-2-naphthalenyl)carbamoyl]benz oic acid (Am80) and 4-[(5,6,7,8-tetrahydro-5,5,8,8-tetramethyl-2-naphthalenyl)carboxamido] benzoic acid (Am580) were several times more active than retinoic acid in the assay. They are structurally related to retinoic acid, as is clear from the biological activity of the hybrid compounds (M2 and R2).

Amides↗
PubMed2003

Antineoplastic agents. 487. Synthesis and biological evaluation of the antineoplastic agent 3,4-methylenedioxy-5,4'-dimethoxy-3'-amino-Z-stilbene and derived amino acid amides.

An efficient synthesis of 3,4-methylenedioxy-5,4'-dimethoxy-3'-amino-Z-stilbene (1c) and hydrochloride (1d) is reported. The nitrostilbene intermediate 6a was obtained via a Wittig reaction using phosphonium salt 4 and 3-nitro-4-methoxybenzaldehyde 5. A one-step reduction using zinc in acetic acid produced the synthetic objective amine 1c. The coupling of this amine with various Fmoc amino acids, followed by cleavage of the alpha-amine protecting group, resulted in a series of new cancer cell growth inhibitory amides. Amine 1c, hydrochloride 1d, glycine amide 3b, and tyrosine amide 3f had the highest level (GI50 = 10(-2)-10(-3) micro g/mL) of activity against a panel of six human and one animal (P388) cancer cell lines. Amine 1c and its hydrochloride 1d potently inhibited tubulin polymerization by binding at the colchicine site, while the amides had little activity against purified tubulin. Nevertheless, most of the amides caused a marked increase in the mitotic index of treated cells, indicating that tubulin was their intracellular target.

Amides↗
PubMed2005

Optimization of amide-based inhibitors of soluble epoxide hydrolase with improved water solubility.

Soluble epoxide hydrolase (sEH) plays an important role in the metabolism of endogenous chemical mediators involved in the regulation of blood pressure and inflammation. 1,3-Disubstituted ureas with a polar group located on the fifth atom from the carbonyl group of urea function are active inhibitors of sEH both in vitro and in vivo. However, their limited solubility in water and relatively high melting point lead to difficulties in formulating the compounds and poor in vivo efficacy. To improve these physical properties, the effect of structural modification of the urea pharmacophore on the inhibition potencies, water solubilities, octanol/water partition coefficients (log P), and melting points of a series of compounds was evaluated. For murine sEH, no loss of inhibition potency was observed when the urea pharmacophore was modified to an amide function, while for human sEH 2.5-fold decreased inhibition was obtained in the amide compounds. In addition, a NH group on the right side of carbonyl group of the amide pharmacophore substituted with an adamantyl group (such as compound 14) and a methylene carbon present between the adamantyl and amide groups were essential to produce potent inhibition of sEH. The resulting amide inhibitors have 10-30-fold better solubility and lower melting point than the corresponding urea compounds. These findings will facilitate synthesis of sEH inhibitors that are easier to formulate and more bioavailable.

1-Octanol↗
PubMed2005

Conformation analyses, dynamic behavior, and amide bond distortions of medium-sized heterocycles. 2. Partially and fully reduced 1-benzazocines, benzazonines, and benzazecines.

Partially and fully reduced forms of benzo-fused eight- to ten-membered nitrogen heterocycles (1-benzazecines, 1-benzazonines and 1-benzazecines) have been prepared. Conformational features, transannular distances and dynamic behavior were studied using X-ray crystallography and VT NMR spectroscopy. The amide moiety in the nine-membered benzazonine ring 5b favors N-pyramidization, whereas the ten-membered benzazecine 5c adopts an amide twist. Molecular mechanics calculations reveals a correlation between the amide twist (tau) and ring stability. The dynamic behavior of the heterocycles in solution were also found to be dependent on the extent and nature of the amide distortion. We thus conclude that ring strain of these medium-sized heterocyclic rings is relieved through amide distortion, which leads to a more stable structure.

Amides↗
PubMed2005

Synthesis of structurally defined scaffolds for bivalent ligand display based on glucuronic acid anilides. The degree of tertiary amide isomerism and folding depends on the configuration of a glycosyl azide.

[structures: see text] Syntheses and structural analyses of bivalent carbohydrates based on anilides of glucuronic acid are described. Secondary anilides predominantly adopted the Z-anti structure; there is also evidence for population of the Z-syn isomer. Bivalent tertiary anilides displayed two signal sets in their NMR spectra, consistent with the presence of (i) a major isomer where both amides have E configurations (EE) and (ii) a minor isomer where one amide is E and the other Z (EZ). Qualitative NOE/ROE spectroscopic studies in solution support the proposal that the anti conformation is preferred for E amides. The crystal structure of one bivalent tertiary anilide showed E-anti and E-syn structural isomers; intramolecular carbohydrate-carbohydrate stacking was observed and mediated by carbonyl-pyranose, azide-azide, and pyranose-aromatic interactions. The EE to EZ isomer ratio, or the degree of folding, for tertiary amides, was greatest for a bivalent compound containing two alpha-glycosyl azide groups; this was enhanced in water, suggesting that hydrophobic interactions are partially but not wholly responsible. Computational methods predicted azide-aromatic (N...H-C interaction) and azide-azide interactions for folded isomers. The close contact of the azide and aromatic protons (N...H-C interaction) was observed upon examination of the close packing in the crystal structure of a related monomer. It is proposed that the alpha-azide group is more optimally aligned, compared to the beta-azide, to facilitate interaction and minimize the surface area of the hydrophobic groups exposed to water, and this leads to the increased folding. The alkylation of bivalent secondary anilides induces a switch from Z to E amide that alters the scaffold orientation. The synthesis of a bivalent mannoside, based on a secondary anilide scaffold, for investigation of mannose-binding receptor cross-linking and lattice formation is described.

Amides↗
PubMed2006

Traceless Staudinger ligation of glycosyl azides with triaryl phosphines: stereoselective synthesis of glycosyl amides.

Alpha-glycosyl amides can be synthesized from the corresponding O-benzyl-alpha-glycosyl azides using a traceless Staudinger ligation with diphenylphosphanyl-phenyl esters 4. All the phosphines employed and their phenol precursors are stable to air at 4 degrees C for months. Fast intramolecular trapping of the reduction intermediates results in the direct formation of the amide link, which, in turn, prevents epimerisation and allows retention of configuration at the anomeric carbon. Yields and alpha-selectivity are high when the reaction is performed in polar aprotic solvents. Removal of the benzyl ether protecting groups is achieved by catalytic hydrogenation. Alpha-glycosyl amides represent a class of virtually unexplored nonhydrolyzable monosaccharide derivatives that may find a useful application as sugar mimics. Conformational studies by NMR spectroscopy confirm that deprotected alpha-glycosyl amides in the gluco, galacto, and fuco series retain the normal pyranose conformation of the monosaccharide. The reaction of phosphines 4 with tetra-O-acetyl-glycosyl azides is nonstereoconservative, and beta-glycosyl amides are obtained in good yields and with complete stereoselectivity starting from both alpha and beta azides.

Amides↗
PubMed2007

Amide bond cleavage: acceleration due to a 1,3-diaxial interaction with a carboxylic acid.

To independently assess the contribution of ground-state pseudoallylic strain to the enormous rates of amide bond cleavage in tertiary amide derivatives of Kemp's triacid, we have studied four amide derivatives of (1alpha-3alpha-5beta)-5-tert-butyl-1,3-cyclohexanedicarboxylic acid. Our results demonstrate that absent pseudoallylic strain, a 1,3-diaxial interaction of an amide with a carboxylic acid leads to only a 2400-fold increase in the rate of amide bond cleavage as compared with the rate of hydrolysis of an unactivated peptide bond.

Amides↗
PubMed2005

All-atom molecular dynamic simulations and relative NMR spectra study of weak C-H...O contacts in amide-water systems.

Amide-water mixtures are studied by all-atom molecular dynamics (MD) simulations and the relative temperature-dependent NMR experiment. The weak C-H...O contacts are found in the amide-water systems theoretically and experimentally. The statistical results of the average numbers of hydrogen bonds indicate that the methyl groups in amide molecules represent different capabilities in forming the weak C-H...O contacts. The statistics also imply that the C-H...O contacts are more obvious in the amide-rich region than those in the water-rich region. The temperature-dependent NMR spectra are also adopted to investigate the weak C-H...O contacts in the amide-water systems. The relative chemical shifts of the methyl groups are in good agreement with the MD simulations.

Amides↗
PubMed2005

Ab initio modeling of amide I coupling in antiparallel beta-sheets and the effect of 13C isotopic labeling on infrared spectra.

Isotopic substitution with 13C on the amide C=O has become an important means of determining localized structural information about peptide conformations with vibrational spectroscopy. Various approaches to the modeling of the interactions between labeled amide sites, specifically for antiparallel two-stranded, beta-forming peptides, were investigated, including different force fields [dipole-dipole interaction vs density functional theory (DFT) treatments], basis sets, and sizes of model peptides used for ab initio calculations, as well as employing models of solvation. For these beta-sheet systems the effect of the relative positions of the 13C isotopic labels in each strand on their infrared spectra was investigated. The results suggest that the interaction between labeled amide groups in different strands can be used as an indicator of local beta-structure formation, because coupling between close-lying C=O groups on opposing chains leads to the largest frequency shifts, yet some alternate placements can lead to intensity enhancements. The basic character of the coupling interaction between labeled modes on opposing strands is independent of changes in peptide length, water solvent environment, twisting of the sheet structure, and basis set used in the calculations, although the absolute frequencies and detailed coupling magnitudes change under each of these perturbations. In particular, two strands of three amides each contain the basic interactions needed to simulate larger sheets, with the only exception that the C=O groups forming H-bonded rings at the termini can yield different coupling values than central ones of the same structure. Spectral frequencies and intensities were modeled ab initio by DFT primarily at the BPW91/6-31G** level for pairs of three, four, and six amide strands. Comparison to predictions of a classical coupled oscillator model show qualitative but not quantitative agreement with these DFT results.

Amides↗
PubMed2005

Amide I vibrational dynamics of N-methylacetamide in polar solvents: the role of electrostatic interactions.

The vibrational frequency of the amide I transition of peptides is known to be sensitive to the strength of its hydrogen bonding interactions. In an effort to account for interactions with hydrogen bonding solvents in terms of electrostatics, we study the vibrational dynamics of the amide I coordinate of N-methylacetamide in prototypical polar solvents: D2O, CDCl3, and DMSO-d6. These three solvents have varying hydrogen bonding strengths, and provide three distinct solvent environments for the amide group. The frequency-frequency correlation function, the orientational correlation function, and the vibrational relaxation rate of the amide I vibration in each solvent are retrieved by using three-pulse vibrational photon echoes, two-dimensional infrared spectroscopy, and pump-probe spectroscopy. Direct comparisons are made to molecular dynamics simulations. We find good quantitative agreement between the experimentally retrieved and simulated correlation functions over all time scales when the solute-solvent interactions are determined from the electrostatic potential between the solvent and the atomic sites of the amide group.

Amides↗
PubMed1997

Specific induction of the hsr omega locus of Drosophila melanogaster by amides.

We report here that 3-aminobenzamide and other amides, such as formamide, acetamide and nicotinamide, specifically induce a high rate of transcription at the 93D puff (the hsr omega heat shock gene) in polytene chromosomes of Drosophila melanogaster. Other chemicals, such as benzamide, colchicine, thiamphenicol and paracetamol, that are already known to specifically induce transcription at the hsr omega locus are also identified as amides. In view of the specific induction of the 93D puff by different amides and other data that demonstrate hsr omega transcription in response to benzamide and colchicine etc. to be independent of its heat shock induction, it appears likely that amides induce this locus through distinct regulatory elements that we propose to designate amide response elements (AREs).

Acetamides↗
PubMed2003

Cuticular lipids of the booklouse, Liposcelis bostrychophila: hydrocarbons, aldehydes, fatty acids, and fatty acid amides.

The booklouse, Liposcelis bostrychophila, is an increasingly common pest of stored food products worldwide. We report here the cuticular lipid composition of this pest (the first report of the hydrocarbons of any member of the Order Psocoptera and the first report of fatty acid amides as cuticular components for any insect). No unsaturated hydrocarbons were present. A homologous series of n-alkanes (C21-C34), monomethyl alkanes (3-, 4-, 5-, 7-, 9-, 11-, 12-, 13- and 15-methyl-) with a carbon chain range of C28-C42, and dimethyl alkanes (3, 7-; 9, 13-; 11, 15-; 13, 17-; 9, 21-; 11, 19-; and 13, 21-) with a carbon number range of C31-C41 were identified. The relative abundances of these hydrocarbons were low, comprising approximately 0.0125% of total biomass. The amides were a homologous series (C16-C22 in chain length), with the major amide being stearoyl amide. In addition to the amides, free fatty acids (C16:1, C16:0, C18:2, C18:1, and C18:0 in chain length) and three straight chain aldehydes (C15, C16, and C17:1 in chain length) also occurred as cuticular components. These findings are discussed in terms of the chemical and physiological ecology of this species.

Aldehydes↗