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PubMed1989

Magainin 2 amide and analogues. Antimicrobial activity, membrane depolarization and susceptibility to proteolysis.

We compared the abilities of synthetic magainin 2 amide and its analogues to inhibit the growth of Escherichia coli and to cause membrane depolarization in E. coli cells and cytochrome oxidase liposomes. The analogue, magainin A, was about 40-times more active than magainin 2 amide in inhibiting the growth of E. coli and had a much more sustained effect on the membrane potential. In the liposomal system, however, there was only approx. 20% difference between these two peptides in the reduction of membrane potential and uncoupling of respiration. Studies with pronase digestion suggested that the difference in potency may be due to differential susceptibility to proteolysis in the presence of membranes.

Amides↗
PubMed1984

Amide proton titration shifts in bull seminal inhibitor IIA by two-dimensional correlated 1H nuclear magnetic resonance (COSY). Manifestation of conformational equilibria involving carboxylate groups.

Amide proton titration shifts in H2O solution of bull seminal inhibitor IIA were measured over the pH range from 3 to 6 using two-dimensional correlated spectroscopy. These data enabled characterization of the pKa values for the majority of the carboxylate groups in the protein. Two glutamate side-chains were found to form hydrogen bonds with their own backbone amide proton. Different temperature variations of the populations of these local, cyclic structure elements are indicated for the individual sites.

Amides↗
PubMed1990

Amide proton exchange in human metallothionein-2 measured by nuclear magnetic resonance spectroscopy.

In human metallothionein-2, the exchange rate constants of ten amide protons were found to range from 1.7 x 10(-4) to 1 x 10(-1) min-1 at pH 6.3 and 8 degrees C. Most of these slowly exchanging protons could be associated with hydrogen bonds in secondary structure elements of the alpha-domain. Amide proton exchange rates thus present an additional criterion for the structural characterization of different metallothioneins, which could be particularly valuable for comparisons of different homologous protein preparations containing nuclear magnetic resonance-inactive metal ions, where the metal-polypeptide co-ordinative bonds cannot be identified directly.

Amides↗
PubMed1992

Identification of a protein-binding surface by differential amide hydrogen-exchange measurements. Application to Bowman-Birk serine-protease inhibitor.

The binding surface of soybean trypsin/chymotrypsin Bowman-Birk inhibitor in contact with alpha-chymotrypsin has been identified by measurement of the change in amide hydrogen-exchange rates between free and chymotrypsin-bound inhibitor. Exchange measurements were made for the enzyme-bound form of the inhibitor at pH 7.3, 25 degrees C using fast-flow affinity chromatography and direct measurement of exchange rates in the protein complex from one-dimensional and two-dimensional nuclear magnetic resonance spectra. The interface is characterized by a broad surface of contact involving residues 39 through 48 of the anti-chymotryptic domain beta-hairpin as well as residues 32, 33 and 37 in the anti-chymotryptic domain loop of the inhibitor. A number of residues in the anti-tryptic domain of the protein also have an altered exchange rate, suggesting that there are changes in the protein conformation upon binding to chymotrypsin. These changes in amide exchange behavior are discussed in light of a model of the complex based on the X-ray crystallographic structure of turkey ovomucoid inhibitor third domain bound to a alpha-chymotrypsin, and the structure of free Bowman-Birk inhibitor determined in solution by two-dimensional nuclear magnetic resonance spectroscopy. The chymotrypsin-binding loop of Bowman-Birk inhibitor in the model is remarkably similar to the binding loop conformation in crystal structures of enzyme-bound polypeptide chymotrypsin inhibitor-I from potatoes, turkey ovomucoid inhibitor third domain, and chymotrypsin inhibitor-II from barley seeds.

Amides↗
PubMed1985

Binding of ester and amide epimers of 20 zeta-dihydroprednisolonic acid to cytosol receptors and their acute pharmacological activities in rats.

The competitive binding of two new classes of anti-inflammatory steroids, the esters and amides derived from the epimers of 20 zeta-dihydroprednisolonic acid, to cytosol receptors from rat liver and thymus was studied. The relative inhibition of [3H]dexamethasone binding by the steroid derivatives was the same, irrespective of the receptor source, with the following order: dexamethasone greater than prednisolone greater than methyl 17,20 alpha-acetonidodihydroprednisolonate greater than methyl 17,20 beta-acetonidodihydroprednisolonate greater than N-propyl 20 alpha-dihydroprednisolonamide greater than methyl 20 alpha-dihydroprednisolonate greater than methyl 20 beta-dihydroprednisolonate greater than N-propyl 20 beta-dihydroprednisolonamide. The alpha-epimer of the steroids always showed a higher binding affinity than the corresponding beta-epimer. In an acute pharmacological study, prednisolone induced the suppression of plasma corticosterone and an increase in tyrosine aminotransferase activity and glycogen content of rat liver. The esters and amides had no effect on these parameters except in the case of the acetonide derivatives of the steroid acid esters which slightly increased liver glycogen content.

Amides↗
PubMed1983

Deviation from Michaelis-Menten kinetics for esterase E-II from the venom of Bitis gabonica, using synthetic arginine amides as substrates.

Steady state kinetic studies on the reaction between esterase E-II from the venom of Bitis gabonica and the fluorogenic substrates, N-alpha-benzoyl-L-phenylalanyl-L-valyl-L-arginine-4-methylcoumaryl-7-amide and N-alpha-benzoyl-L-arginine-4-methylcoumaryl-7-amide were found to deviate from Michaelis-Menten kinetics. Analysis of algebraic graphs and application of non-linear regression allowed an empirical rate law to be selected. The results revealed a rate equation of at least third degree at pH values above 7.0 and of 2:2 degree in the pH range 6-7. The data were interpreted in terms of a molecular model involving an enzyme with one catalytic site and several auxiliary or regulatory sites which, through cooperative effects, may either activate or inhibit the enzyme. Substrate activation is observed at low substrate values and might follow from an obligatory order of binding involving two of the sites, the modifier substrate molecule binding before the substrate molecule undergoing transformation to products. Inhibitory sites apparently become available only at alkaline pH. The inhibition is only noted at high substrate concentrations and is of the partial type.

Amides↗
PubMed1995

The liquid amide transfer model and the unfolding thermodynamics of small globular proteins.

In this paper, the solid cyclic dipeptide model developed by Murphy and Gill is analysed in order to point out that, apart from general thermodynamic features shown by well-characterized small globular proteins, only the polar and apolar contributions to the net denaturation heat capacity change are necessary to calculate the so-called protein stability curve, delta dGzero versus temperature. We propose that these specific heat capacity contributions can be determined in a reliable manner by a group additivity analysis of the transfer process of liquid amides from pure liquid phase into water. This suggests that the unfolding process, thought of as the transfer of amino acid residues from the protein 'core' to contact with water molecules, can be modelled based on the transfer process of organic amides. The reliability of the model is tested in comparison with literature data.

Amides↗
PubMed1985

Assignment of amides in the amino acid sequence of mammalian calmodulin by mass spectrometry.

The primary structure of mammalian calmodulin from various sources was analyzed by secondary ion mass spectrometry. The assignments of amide groups at residues 24, 60, 129 and 135, which had been controversial in the previous reports, were in perfect agreement with the amino acid sequence deduced from the cDNA sequence of calmodulin of other vertebrates. The result is against the post-translational amidation or deamidation process of this protein.

Amides↗
PubMedDate not supplied

Chemical stability and plasma-catalyzed dealkylation of peptidyl-alpha-hydroxyglycine derivatives--intermediates in peptide alpha-amidation.

The production of alpha-amidated peptides has recently been shown to occur via a two-step process with peptidyl-alpha-hydroxyglycine being an intermediate. In this study the chemical stability and plasma-catalyzed conversion of various peptidyl-alpha-hydroxyglycine derivatives to their parent amide product have been examined. This conversion was shown to be independent of pH in the range pH 1-5 and to be apparently specific base-catalyzed at pH 6-10. At pH 7.4 and 37 degrees C the half-lives of decomposition of the derivatives ranged from 5.8 to 13.3 h. In 80% human plasma solutions (pH 7.4) the half-lives decreased to 1.3-3.9 h, indicating the occurrence of an enzyme activity in plasma catalyzing the dealkylation of peptidyl-alpha-hydroxyglycine derivatives. The best substrate for the plasma catalytic activity was found to be N-benzyloxycarbonyl-L-alanyl-alpha-hydroxyglycine.

Alkylation↗
PubMed1989

Effect of protein side chain amide group on the hydrogen-bond equilibrium in nucleobases studied by infrared and 13C-NMR spectroscopy.

Infrared spectra of 1:1 hydrogen-bonded complexes formed by derivatives of adenine and model molecules bearing the protein side chain amide group have been measured in chloroform solution. From the temperature dependence of hydrogen-bond formation, thermodynamic data on these complexes are determined. On the basis of these data, it is shown that the complexes consist of cyclic heterodimers, those that use the adenine N(1)H bond being favoured. Similarly infrared and 13C-NMR spectroscopy reveals that uracil-amide cyclic heterodimers formed through the uracil 4-carbonyl group are predominant. All of these results predict that Watson-Crick hydrogen bonds in adenine-uracil base-pairs may be opened to some extent, as proved in this work. The possible biological importance of these observations is also discussed.

Acetamides↗
PubMed1995

Amides of piperidine, morpholine and piperazine substituted 1-phenylethylamines: inhibitors of acylCoA:cholesterol acyltransferase (ACAT) activity in vitro and in vivo.

Amides of some substituted 1,2-diarylethylamines have been shown to exhibit potent acylCoA:cholesterol acyltransferase (ACAT, EC 2.3.1.26) inhibitory activity in vitro in microsomal ACAT assays but show poor in vivo activity in a cholesterol-fed hamster model. In an effort to design ACAT inhibitors that are potent in both our in vitro and in vivo assays a series of amides of piperidine, morpholine and piperazine substituted 1-phenylethylamines were synthesized. Compounds of this series were found to be very potent inhibitors of ACAT in a microsomal ACAT assay and also exhibited potent activity in a cholesterol-fed hamster model.

Amides↗
PubMed1995

Amide and alpha-keto carbonyl inhibitors of thrombin based on arginine and lysine: synthesis, stability and biological characterization.

We report structure-activity investigations in a series of tripeptide amide inhibitors of thrombin, and the development of a series of highly potent active site directed alpha-keto carbonyl inhibitors having the side chain of lysine at P1. Compounds of this class are unstable by virtue of reactivity at the electrophilic carbonyl and racemization at the adjacent carbon (CH). Modifications of prototype alpha-keto-ester 8a have afforded analogs retaining nanomolar Ki. Optimal potency and stability have been realized in alpha-keto-amides 11b (Ki = 2.8 nM) and 11c (Ki = 0.25 nM).

Amides↗
PubMed1996

The synthesis of peptidomimetic combinatorial libraries through successive amide alkylations.

A soluble peptidomimetic combinatorial library of 57,500 compounds was prepared. This library has a dipeptide scaffold with each amide hydrogen replaced with five different alkyl groups (methyl, ethyl, allyl, benzyl, or naphthylmethyl). Solid-phase methodology in combination with N-alkylation were used to synthesize the library, which incorporated 50 different L-, D-, and unnatural amino acids. Repetitive amide alkylations were carried out on the solid support following each amino acid coupling step. Individual model compounds were synthesized in order to optimize the alkylation conditions, to study potential amino acid side chain modifications, to determine the extent of racemization, and to provide analytical controls during the library synthesis.

Alkylation↗
PubMed2005

A fluorescence-based assay for fatty acid amide hydrolase compatible with high-throughput screening.

A novel fluorescent assay to continuously monitor fatty acid amide hydrolase (FAAH) activity that is simple, sensitive, and amenable to high-throughput screening (HTS) of compound libraries is described in this article. Stable Chinese hamster ovary (CHO) cell lines expressing either human FAAH or an inactive mutant, FAAH-S241A, were established. Arachidonyl 7-amino, 4-methyl coumarin amide (AAMCA), a novel fluorogenic substrate for FAAH, was designed and synthesized. FAAH catalyzes the hydrolysis of AAMCA to generate arachidonic acid and a highly fluorescent 7-amino, 4-methyl coumarin (AMC). The assay was done at 25 degrees C by incubating whole cell or microsomal preparations from FAAH-expressing cells with AAMCA. Release of AMC was monitored continuously using a fluorometer. Microsomal FAAH catalyzed the hydrolysis of AAMCA with an apparent K(m) of 0.48muM and V(max) of 58pmolmin(-1)mgprotein(-1). The assay is specific for FAAH given that microsomes prepared from cells expressing FAAH-S241A or vector alone had no significant activity against AAMCA. Furthermore, the activity was inhibited by URB-597, an FAAH-specific inhibitor, in a concentration-dependent manner with an IC(50) of 33.5nM. The assay was optimized for HTS and had a Z' value ranging from 0.7 to 0.9. The assay is also compatible with ex vivo analysis of FAAH activity.

Amidohydrolases↗
PubMed2005

Insights into enzyme structure and dynamics elucidated by amide H/D exchange mass spectrometry.

Conformational changes and protein dynamics play an important role in the catalytic efficiency of enzymes. Amide H/D exchange mass spectrometry (H/D exchange MS) is emerging as an efficient technique to study the local and global changes in protein structure and dynamics due to ligand binding, protein activation-inactivation by modification, and protein-protein interactions. By monitoring the selective exchange of hydrogen for deuterium along a peptide backbone, this sensitive technique probes protein motions and structural elements that may be relevant to allostery and function. In this report, several applications of H/D exchange MS are presented which demonstrate the unique capability of amide hydrogen/deuterium exchange mass spectrometry for examining dynamic and structural changes associated with enzyme catalysis.

Amides↗
PubMed2005

Amides as cryoprotectants for freezing stallion semen: a review.

Stallion semen cryopreservation, despite its impact on the horse industry, is not an established technology. During the last years, a number of modifications have been proposed to the freezing process, however, a large population of stallions still have poor semen quality and fertility after frozen-thawed. Glycerol toxicity could be a reason for the variation on stallion sperm freezability. There are limited publications concerning the use of alternative cryoprotectants for equine sperm. Glycerol is contraceptive for some species and other cryoprotectors, such as amides, have been show to be a good option for freezing semen of these species. Recent reports have shown encouraging data respecting the use of amides as cryoprotectants for stallions, with more remarkable improvements for semen from stallions that freeze poorly when glycerol is used.

Amides↗
PubMed2004

Synthesis of N-(beta-D-glucopyranosyl)- and N-(2-acetamido-2-deoxy-beta-D-glucopyranosyl) amides as inhibitors of glycogen phosphorylase.

2,3,4,6-Tetra-O-acetyl-beta-D-glucopyranosyl- and 2-acetamido-3,4,6-tri-O-acetyl-2-deoxy-beta-D-glucopyranosyl azides were transformed into the corresponding per-O-acetylated N-(beta-D-glycopyranosyl) amides via a PMe(3) mediated Staudinger protocol (generation of N-(beta-D-glycopyranosyl)imino-trimethylphosphoranes followed by acylation with carboxylic acids, acid chlorides or anhydrides). The deprotected compounds obtained by Zemplén deacetylation were evaluated as inhibitors of rabbit muscle glycogen phosphorylase b. The best inhibitor of this series has been N-(beta-D-glucopyranosyl) 3-(2-naphthyl)-propenoic amide (K(i)=3.5microM).

Amides↗
PubMed2005

Synthesis and potent antimicrobial activity of some novel methyl or ethyl 1H-benzimidazole-5-carboxylates derivatives carrying amide or amidine groups.

A series of benzimidazole-5-carboxylic acid alkyl ester derivatives carrying amide or amidine substituted methyl or phenyl groups at the position C-2 were synthesised and evaluated for antibacterial and antifungal activities against S. aureus, methicillin resistant S. aureus (MRSA), S. faecalis, methicillin resistant S. epidermidis (MRSE), E. coli and C. albicans. The results showed that while all simple acetamides are essentially inactive, aromatic amides and amidines have potent antibacterial activities. Aromatic amidine derivatives 13 f-h exhibited the best inhibitory activity with 1.56-0.39 microg/mL MIC values against MRSA and MRSE.

Amides↗