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PubMed2001

Inhibition of human platelet aggregation by amides and ester of salicylic acid with platelet-activating factor analogs.

The influence of acetyl salicylic acid (ASA) derivatives with platelet-activating factor (PAF) lipid analogs on PAF-induced human platelet aggregation has been studied. It was found that the ASA amide with an ethanolamine plasmalogen PAF analog (1-0-alk-1'-enyl-2-acetyl-sn-glycero-3-phospho-(N-2'-acetoxybenzoyl)ethanolamine) and the ASA ester with a choline plasmalogen PAF analog (1-0-alk-1'-enyl-2-(2'-acetoxybenzoyl)-sn-glycero-3-phosphocholine) at concentrations of 10-7-10-6 M effectively inhibit PAF-induced aggregation of human platelets. In contrast to these compounds, the ASA amide with an alkyl PAF analog (1-0-alkyl-2-acetyl-sn-glycero-3-phospho-(N-2'-acetoxybenzoyl)ethanolamine) did not inhibit PAF-induced platelet aggregation. As possible mechanisms of action of the studied compounds, the blockade of PAF-receptor and cyclooxygenase inhibition are proposed.

Amides↗
PubMed1994

Solubility predictions for solid nitriles and tertiary amides based on the mobile order theory.

The solubilities of hexadecanenitrile, octadecanenitrile, N,N-diphenyl capramide, and N,N-diphenyl lauramide are predicted in common organic nonelectrolyte solvents using the solubility equation derived from the mobile order theory. In the framework of this theory, the formation of hydrogen bonds is treated on the basis of stability constants. Two values characterizing the nitrile-alcohol and the tertiary amide-alcohol hydrogen bonds, 175 and 600 cm3 mol-1, respectively, are determined. Although the formation of solute-solvent specific molecular interactions brings about a net increase in the solubility, the solubilities of the nitriles and amides in alcohols remain lower than those measured in nonassociated solvents because of the large negative hydrophobic effect of the alcohol molecules.

Amides↗
PubMed2003

Assignment of amide proton signals by combined evaluation of HN, NN and HNCA MAS-NMR correlation spectra.

In this paper, we present a strategy for the (1)H(N) resonance assignment in solid-state magic-angle spinning (MAS) NMR, using the alpha-spectrin SH3 domain as an example. A novel 3D triple resonance experiment is presented that yields intraresidue H(N)-N-C(alpha) correlations, which was essential for the proton assignment. For the observable residues, 52 out of the 54 amide proton resonances were assigned from 2D ((1)H-(15)N) and 3D ((1)H-(15)N-(13)C) heteronuclear correlation spectra. It is demonstrated that proton-driven spin diffusion (PDSD) experiments recorded with long mixing times (4 s) are helpful for confirming the assignment of the protein backbone (15)N resonances and as an aid in the amide proton assignment.

Amides↗
PubMed2003

Extending the range of amide proton relaxation dispersion experiments in proteins using a constant-time relaxation-compensated CPMG approach.

Relaxation compensated constant-time Carr-Purcell-Meiboom-Gill relaxation dispersion experiments for amide protons are presented that detect mus-ms time-scale dynamics of protein backbone amide sites. Because of their ten-fold larger magnetogyric ratio, much shorter 180 degrees pulses can be applied to (1)H than to (15)N spins; therefore, off-resonance effects are reduced and a wider range of effective rf fields can often be used in the case of (1)H experiments. Applications to [(1)H-(15)N]-ubiquitin and [(1)H-(15)N]-perdeuterated HIV-1 protease are discussed. In the case of ubiquitin, we present a pulse sequence that reduces artifacts that arise from homonuclear (3)J(H(N)-H(alpha)) coupling. In the case of the protease, we show that relaxation dispersion of both (1)H and (15)N spins provides a more comprehensive picture of slow backbone dynamics than does the relaxation dispersion of either spin alone. We also compare the relative merits of (1)H versus (15)N transverse relaxation measurements and note the benefits of using a perdeuterated protein to measure the relaxation dispersion of both spin types.

Amides↗
PubMedDate not supplied

[Synthesis and antiviral activity of amides and conjugates of betulonic acid with amino acids].

Betulonic acid amides with aliphatic and heterocyclic amines and with L-amino acids were synthesized by the acid chloride method. Betulonic acid amide and L-methionine derivatives of betulonic acid and its 3-oxime effectively inhibit the influenza A virus. Betulonic acid octadecylamide is active against the herpes simplex type 1 virus. The conjugate of betulonic acid 3-oxime with L-methionine is also active toward HIV-1. The tested compounds mainly show no activity toward the ECHO6 virus, which is devoid of a coat. The English version of the paper: Russian Journal of Bioorganic Chemistry, 2004, vol. 30, no. 1; see also http://www.maik.ru.

Amides↗
PubMed1999

Cysteic- and homocysteic acid-S-(aminoiminomethyl) amides: a new class of modified arginines useful in peptide synthesis.

A novel, practical synthesis of the title compounds and their derivatives are described. The protecting groups for amino, guanidino and carboxylic functions of substituted amides of cysteic and homocysteic acid were selected with the aim of making the amino acid derivatives synthons for peptide synthesis both in solution and by the solid phase method. Studying the structure-activity relationship some new kyotorphin, [Leu] kyotorphin and MIF-1 analogues, containing the unusual amino acid cysteic acid-S-(aminoiminomethyl) amide (sArg) in position two, have been prepared. It is a very promising compound, a structural analogue of arginine and an efficient antagonist in its metabolism.

Amides↗
PubMed2000

Domain-specific recruitment of amide amino acids for protein synthesis.

The formation of aminoacyl-transfer RNA is a crucial step in ensuring the accuracy of protein synthesis. Despite the central importance of this process in all living organisms, it remains unknown how archaea and some bacteria synthesize Asn-tRNA and Gln-tRNA. These amide aminoacyl-tRNAs can be formed by the direct acylation of tRNA, catalysed by asparaginyl-tRNA synthetase and glutaminyl-tRNA synthetase, respectively. A separate, indirect pathway involves the formation of mis-acylated Asp-tRNA(Asn) or Glu-tRNA(Gln), and the subsequent amidation of these amino acids while they are bound to tRNA, which is catalysed by amidotransferases. Here we show that all archaea possess an archaea-specific heterodimeric amidotransferase (encoded by gatD and gatE) for Gln-tRNA formation. However, Asn-tRNA synthesis in archaea is divergent: some archaea use asparaginyl-tRNA synthetase, whereas others use a heterotrimeric amidotransferase (encoded by the gatA, gatB and gatC genes). Because bacteria primarily use transamidation, and the eukaryal cytoplasm uses glutaminyl-tRNA synthetase, it appears that the three domains use different mechanisms for Gln-tRNA synthesis; as such, this is the only known step in protein synthesis where all three domains have diverged. Closer inspection of the two amidotransferases reveals that each of them recruited a metabolic enzyme to aid its function; this provides direct evidence for a relationship between amino-acid metabolism and protein biosynthesis.

Amides↗
PubMed2003

Redox regulation of protein tyrosine phosphatase 1B involves a sulphenyl-amide intermediate.

The second messenger hydrogen peroxide is required for optimal activation of numerous signal transduction pathways, particularly those mediated by protein tyrosine kinases. One mechanism by which hydrogen peroxide regulates cellular processes is the transient inhibition of protein tyrosine phosphatases through the reversible oxidization of their catalytic cysteine, which suppresses protein dephosphorylation. Here we describe a structural analysis of the redox-dependent regulation of protein tyrosine phosphatase 1B (PTP1B), which is reversibly inhibited by oxidation after cells are stimulated with insulin and epidermal growth factor. The sulphenic acid intermediate produced in response to PTP1B oxidation is rapidly converted into a previously unknown sulphenyl-amide species, in which the sulphur atom of the catalytic cysteine is covalently linked to the main chain nitrogen of an adjacent residue. Oxidation of PTP1B to the sulphenyl-amide form is accompanied by large conformational changes in the catalytic site that inhibit substrate binding. We propose that this unusual protein modification both protects the active-site cysteine residue of PTP1B from irreversible oxidation to sulphonic acid and permits redox regulation of the enzyme by promoting its reversible reduction by thiols.

Amides↗
PubMed2005

Inhibition of fatty acid amide hydrolase and monoacylglycerol lipase by the anandamide uptake inhibitor VDM11: evidence that VDM11 acts as an FAAH substrate.

There is some dispute concerning the extent to which the uptake inhibitor VDM11 (N-(4-hydroxy-2-methylphenyl) arachidonoyl amide) is capable of inhibiting the metabolism of the endocannabinoid anandamide (AEA) by fatty acid amide hydrolase (FAAH). In view of a recent study demonstrating that the closely related compound AM404 (N-(4-hydroxyphenyl)arachidonylamide) is a substrate for FAAH, we re-examined the interaction of VDM11 with FAAH. In the presence of fatty acid-free bovine serum albumin (BSA, 0.125% w v(-1)), both AM404 and VDM11 inhibited the metabolism of AEA by rat brain FAAH with similar potencies (IC(50) values of 2.1 and 2.6 microM, respectively). The compounds were about 10-fold less potent as inhibitors of the metabolism of 2-oleoylglycerol (2-OG) by cytosolic monoacylglycerol lipase (MAGL). The potency of VDM11 towards FAAH was dependent upon the assay concentration of fatty acid-free bovine serum albumin (BSA). Thus, in the absence of fatty acid-free BSA, the IC(50) value for inhibition of FAAH was reduced by a factor of about two (from 2.9 to 1.6 microM). A similar reduction in the IC(50) value for the inhibition of membrane bound MAGL by both this compound (from 14 to 6 microM) and by arachidonoyl serinol (from 24 to 13 microM) was seen. An HPLC assay was set up to measure 4-amino-m-cresol, the hypothesised product of FAAH-catalysed VDM11 hydrolysis. 4-Amino-m-cresol was eluted with a retention time of approximately 2.4 min, but showed a time-dependent degradation to compounds eluting at peaks of approximately 5.6 and approximately 8 min. Peaks with the same retention times were also found following incubation of the membranes with VDM11, but were not seen when the membranes were preincubated with the FAAH inhibitors URB597 (3'-carbamoyl-biphenyl-3-yl-cyclohexylcarbamate) and CAY10401 (1-oxazolo[4,5-b]pyridin-2-yl-9-octadecyn-1-one) prior to addition of VDM11. The rate of metabolism of VDM11 was estimated to be roughly 15-20% of that for anandamide. It is concluded that VDM11 is an inhibitor of FAAH under the assay conditions used here, and that the inhibition may at least in part be a consequence of the compound acting as an alternative substrate.

Amidohydrolases↗
PubMed2004

Asymmetric synthesis and applications of beta-amino Weinreb amides: asymmetric synthesis of (S)-coniine.

Conjugate addition of lithium (S)-N-benzyl-N-alpha-methylbenzylamide to a range of alpha, beta-unsaturated Weinreb amides proceeds with high levels of diastereoselectivity (>95% de). The beta-amino Weinreb amide products may be transformed into beta-amino ketones via reactions with Grignard reagents, while treatment with DIBAL-H furnishes beta-amino aldehydes. Trapping of the aldehyde via Wadsworth-Emmons reaction and subsequent manipulation offers an efficient route to homochiral delta-amino acid derivatives and 2-substituted piperidines. The application of this methodology for the synthesis of (S)-coniine is demonstrated.

Aldehydes↗
PubMed2004

Oligonucleotides with 2'-O-carboxymethyl group: synthesis and 2'-conjugation via amide bond formation on solid phase.

An efficient method for synthesis of oligonucleotide 2'-conjugates via amide bond formation on solid phase is described. Protected oligonucleotides containing a 2'-O-carboxymethyl group were obtained by use of a novel uridine 3'phosphoramidite, where the carboxylic acid moiety was introduced as its allyl ester. This protecting group is stable to the conditions used in solid-phase oligonucleotide assembly, but easily removed by Pd(0) and morpholine treatment. 2'-O-Carboxymethylated oligonucleotides were then efficiently conjugated on a solid support under normal peptide coupling conditions to various amines or to the N-termini of small peptides to give products of high purity in good yield. The method is well suited in principle for the preparation of peptide-oligonucleotide conjugates containing an amide linkage between the 2'-position of an oligonucleotide and the N-terminus of a peptide.

Amides↗
PubMed2004

Rare and unexpected coordination to copper(II) by a tertiary amide in a macrocyclic ligand.

Incorporation of a tertiary amide donor within the framework of a C(2)-symmetric analogue of 1,4,7-triazacyclononane derived from L-valine results in the isolation of a very rare example of a classical Werner copper(II) complex in which tertiary amide coordination occurs; despite the monomeric nature of the complex in the solid state, frozen solution EPR studies reveal the presence of a triplet ground state consistent with a dimeric species.

Amides↗
PubMed2004

Role of the peri-effect in synthesis and reactivity of highly substituted naphthaldehydes: a novel backbone amide linker for solid-phase synthesis.

Handles (linkers) with an aldehyde functionality that permits the anchoring of substrates by reductive amination have, since their first report in the mid-1990s, become widely-used tools in solid-phase synthesis. In the synthesis of peptides, they allow anchoring of the growing peptide chain through a backbone amide, thus giving easy access to C-terminal modified or cyclic peptides. Recently, we described two new handles (NAL-1 and NAL-2) with dialkoxynaphthaldehyde core structures. Here, we describe the design, synthesis and properties of a novel trialkoxynaphthalene-based backbone amide linker (NAL-3). The NAL-3 handle is based on a trialkoxynaphthaldehyde (NALdehyde-3) that was synthesized in nine high-yielding steps from 3-methoxyphenylacetic acid in 51% overall yield. The naphthalene ring system was constructed using a regioselective methanesulfonic acid-catalyzed ring-closing reaction. The tetra-substituted naphthalene derivative 1,3,6-trimethoxynaphthalene-2-carbaldehyde (7) was selectively demethylated in the 1 position using BBr(3). The selectivity of this reaction is discussed, based on the crystal structures of reactant and product, 1-hydroxy-3,6-dimethoxy-naphthalene-2-carbaldehyde (8), and in the context of the peri-effect. The new handle was anchored to an aminomethylated poly(styrene) solid support, followed by assembly of a model dipeptide, then a study of the cleavage properties under acidic conditions was carried out. Surprisingly, the trialkoxynaphthaldehyde-based handle proved less acid-labile than the dialkoxynaphthaldehyde handles, and this fact is discussed with respect to handle design.

Aldehydes↗
PubMed2005

Reaction of the stable silylene Si[(NCH2But)2C6H4-1,2] with lithium amides.

The thermally stable silylene Si[(NCH2But)2C6H4-1,2] 1 undergoes oxidative addition reactions with the lithium amides LiNRR'(R = SiMe3, R' = But; R = SiMe3, R' = C6H3Me2-2,6; R = R' = Me or R = R' = Pri) to afford the new lithium amides Li(THF)2[N(R)Si(SiMe3){(NCH2But)2C6H4-1,2}][R = But2 or R = C6H3Me2-2,6 (3a)] or the new tris(amino)functionalised silyllithiums Li(THF)x[Si{(NCH2But)2C6H4-1,2}NRR'][R = SiMe3, R' = C6H3Me2-2,6, x = 2 (3); R = R'= Me, x = 3 (4) or R = R' = Pri, x = 3 (5)]. Compounds 4 and 5 are stable at ambient temperature but compound 3 is thermally labile and converts into 3a upon heating. The pathway for the formation of 2 and 3 is discussed and the X-ray structures of 2-5 are presented.

Amides↗
PubMed2005

Analogs of the dihydroceramide desaturase inhibitor GT11 modified at the amide function: synthesis and biological activities.

Dihydroceramide desaturase is the last enzyme in the biosynthesis of ceramide de novo. The cyclopropene-containing sphingolipid GT11 is a competitive inhibitor of dihydroceramide desaturase. The biological effects of chemical modification of the GT11 amide linkage are reported in this article. Either N-methyl substitution or replacement of the amide alpha-carbonyl methylene by oxygen result in inactive compounds. In contrast, both urea (3) and thiourea (4) analogs of GT11, as well as three alpha-ketoamides (5-7), did inhibit the desaturation of N-octanoylsphinganine to N-octanoylsphingosine, although with significantly lower potency than GT11. Furthermore, the alpha-ketoamides 5-7 inhibit the acidic ceramidase with similar potencies (IC50 52-83 microM). Inhibition of the neutral/alkaline ceramidase by these compounds requires around 20-fold higher concentrations. Structure-activity relationships and the biological interest of these compounds are discussed.

Amides↗
PubMed2006

The amide oxygen donor. Metal ion coordinating properties of the ligand nitrilotriacetamide. A thermodynamic and crystallographic study.

The metal ion coordinating properties of ntam (nitrilotriacetamide) are reported. The protonation constant (pK) for ntam is 2.6 in 0.1 M NaClO(4) at 25 degrees C. Formation constants (log K(1)) in 0.1 M NaClO(4) at 25 degrees C, determined by (1)H NMR and UV-Vis spectroscopy are: Ca(II), 1.28; Mg(II), 0.4; La(III), 2.30; Pb(II), 3.69; Cd(II), 3.78; Ni(II), 2.38; Cu(II), 3.16. The measured log K(1) values for the ntam complexes are discussed in terms of the low basicity of the N-donor, as evidenced by the pK, and the effect of metal ion size on complex stability. The amide O-donors of ntam lead to the stabilization of complexes of large metal ions (Pb(II), Cd(II), La(III), Ca(II)) relative to log K1 for the NH3 complexes, while for small metal ions (Ni(II), Cu(II)) the amide O-donors lead to destabilization. This is discussed in terms of the role of chelate ring size in controlling metal ion size-based selectivity. The structures of [Pb(ntam)(NO3)2]2 (1) and [Ca2(ntam)3(H2O)2](ClO4)4.3H2O (2) are reported. For 1: triclinic, space group P1, a = 7.4411(16), b = 9.0455(19), c = 11.625(3) A, alpha = 69.976(4), beta = 79.591(4), gamma = 67.045(3) degrees, Z = 2, R = 0.0275. For 2: monoclinic, space group P2(1)/c, a = 10.485(2), b = 11.414(2), c = 38.059(8) A, beta = 92.05(3) degrees, Z = 4, R = 0.0634. Structure 1 is dimeric with two Pb atoms linked by bridging O-donors from the two ntam ligands. The coordination sphere consists of one N-donor and 3 O-donors from the ntam ligand, two O-donors from nitrates, and one bridging O-donor. The variation in bond length suggests a stereochemically active lone pair of electrons on the Pb. Structure 2 consists of two Ca(II) ions held together by 3 bridging O-donors from ntam groups. One Ca is 9-coordinate with two ntam ligands present, plus one bridging O-donor from the other Ca(II) ntam complex. The other Ca is 8-coordinate, with a single coordinated ntam, plus two coordinated H2O molecules, and two bridging O-donors from the other half of the complex. The role of M-O=C bond angles in controlling selectivity for metal ions on the basis of their size is discussed.

Acetamides↗
PubMed2005

Equilibrium and NMR studies on GdIII, YIII, CuII and ZnII complexes of various DTPA-N,N''-bis(amide) ligands. Kinetic stabilities of the gadolinium(III) complexes.

Three DTPA-derivative ligands, the non-substituted DTPA-bis(amide) (L(0)), the mono-substituted DTPA-bis(n-butylamide) (L(1)) and the di-substituted DTPA-bis[bis(n-butylamide)] (L(2)) were synthesized. The stability constants of their Gd3+ complexes (GdL) have been determined by pH-potentiometry with the use of EDTA or DTPA as competing ligands. The endogenous Cu2+ and Zn2+ ions form ML, MHL and M(2)L species. For the complexes CuL(0) and CuL(1) the dissociation of the amide hydrogens (CuLH(-1)) has also been detected. The stability constants of complexes formed with Gd3+, Cu2+ and Zn2+ increase with an increase in the number of butyl substituents in the order ML(0) < ML(1) < ML(2). NMR studies of the diamagnetic YL(0) show the presence of four diastereomers formed by changing the chirality of the terminal nitrogens of their enantiomers. At 323 K, the enantiomerization process, involving the racemization of central nitrogen, falls into the fast exchange range. By the assignment and interpretation of 1H and 13C NMR spectra, the fractions of the diastereomers were found to be equal at pH = 5.8 for YL(0). The kinetic stabilities of GdL(0), GdL(1) and GdL(2) have been characterized by the rates of the exchange reactions occurring between the complexes and Eu3+, Cu2+ or Zn2+. The rates of reaction with Eu3+ are independent of the [Eu3+] and increase with increasing [H+], indicating the rate determining role of the proton assisted dissociation of complexes. The rates of reaction with Cu2+ and Zn2+ increase with rising metal ion concentration, which shows that the exchange can take place with direct attack of Cu2+ or Zn2+ on the complex, via the formation of a dinuclear intermediate. The rates of the proton, Cu2+ and Zn2+ assisted dissociation of Gd3+ complexes decrease with increasing number of the n-butyl substituents, which is presumably the result of steric hindrance hampering the formation or dissociation of the intermediates. The kinetic stabilities of GdL(0) and GdL(1) at pH = 7.4, [Cu2+] = 1 x 10(-6) M and [Zn(2+)] = 1 x 10(-5) M are similar to that of Gd(DTPA)2-, while the complex GdL2 possesses a much higher kinetic stability.

Amides↗