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PubMed2006

C-terminal N-alkylated peptide amides resulting from the linker decomposition of the Rink amide resin: a new cleavage mixture prevents their formation.

Decomposition of the resin linkers during TFA cleavage of the peptides in the Fmoc strategy leads to alkylation of sensitive amino acids. The C-terminal amide alkylation, reported for the first time, is shown to be a major problem in peptide amides synthesized on the Rink amide resin. This side reaction occurs as a result of the Rink amide linker decomposition under TFA treatment of the peptide resin. The use of 1,3-dimethoxybenzene in a cleavage cocktail prevents almost quantitatively formation of C-terminal N-alkylated peptide amides. Oxidized by-product in the tested Cys- and Met-containing peptides were not observed, even if thiols were not used in the cleavage mixture.

Alkylation↗

PubMed2004

Use of reversed phase HP liquid chromatography to assay conversion of N-acylglycines to primary fatty acid amides by peptidylglycine-alpha-amidating monooxygenase.

Primary fatty acid amides (R-CO-NH2) and N-acylglycines (R-CO-NH-CH2-COOH) are classes of compounds that have only recently been isolated and characterized from biological sources. Key questions remain regarding how these lipid amides are produced and degraded in biological systems. Relative to the fatty acids, little has been done to develop methods to separate and quantify the fatty acid amides and N-acylglycines. We describe reversed phase HPLC methods for the separation of C2-C12 primary fatty acid amides and N-acylglycines and also C12-C22 fatty acid amides. Separation within each class occurs primarily on the basis of simple interactions between the acyl chain and the chromatographic stationary phase, but the polar headgroups on these and related fatty acids and N-acylethanolamides modulate the absolute retention in reversed phase mode. We use these methods to measure the enzyme-mediated, two-step conversion of N-octanoylglycine to octanoamide.

Amides↗

PubMed2004

Molecular dynamics of amide ions in potassium amide (KNH2) studied with orientation-dependent deuterium spin lattice relaxation.

The reorientational molecular dynamics of the amide ions were investigated in three different phases of KND2 by means of 2H NMR line-shape analyses of solid-echo, T1Z as well as T1Q distorted spectra in a temperature range of 80-420 K. The correlation times of the amide dynamics cover roughly eight decades in this temperature range. Due to the nonzero asymmetry parameter (eta approximately 0.2) of the electric field gradient tensor the calculation of the orientation-dependent spectral densities Jm(theta, phi) required for the interpretation of the T1Z and T1Q distorted spectra cannot be simplified as in the case eta = 0 and a numerical approach was used for the calculation of Jm(theta, phi), which allows a maximum flexibility for simulating different models of motion. The amide ion dynamics in the low-temperature phase can be described as a superposition of a thermally activated large angle jump of the amide ions about their two-fold axes in an asymmetric four-well potential and strongly anisotropic molecular librations. The asymmetry of the potential surface of the jump process was found to be a function of temperature. Activation energy EA, attempt frequency tau0(-1) and DND bond angle epsilon were determined to 15.5(2) kJ/mol, 62(6) x 10(12) s(-1) and 104.7(3) degrees. In the middle- and high-temperature phases the amide ions perform 90 degrees jumps about the crystallographic four-fold axes. For the high-temperature modification the correlation times were observed to follow an Arrhenius law with EA = 6.3(2) kJ/mol and tau0(-1) = 32(3) x 10(12) s(-1).

Amides↗

PubMed1999

N-acylglycine amidation: implications for the biosynthesis of fatty acid primary amides.

Bifunctional peptidylglycine alpha-amidating enzyme (alpha-AE) catalyzes the O2-dependent conversion of C-terminal glycine-extended prohormones to the active, C-terminal alpha-amidated peptide and glyoxylate. We show that alpha-AE will also catalyze the oxidative cleavage of N-acylglycines, from N-formylglycine to N-arachidonoylglycine. N-Formylglycine is the smallest amide substrate yet reported for alpha-AE. The (V/K)app for N-acylglycine amidation varies approximately 1000-fold, with the (V/K)app increasing as the acyl chain length increases. This effect is largely an effect on the KM,app; the KM,app for N-formylglycine is 23 +/- 0.88 mM, while the KM,app for N-lauroylglycine and longer chain N-acylglycines is in the range of 60-90 microM. For the amidation of N-acetylglycine, N-(tert-butoxycarbonyl)glycine, N-hexanoylglycine, and N-oleoylglycine, the rate of O2 consumption is faster than the rate of glyoxylate production. These results indicate that there must be the initial formation of an oxidized intermediate from the N-acylglycine before glyoxylate is produced. The intermediate is shown to be N-acyl-alpha-hydroxyglycine by two-dimensional 1H-13C heteronuclear multiple quantum coherence (HMQC) NMR.

Adult↗

PubMed2002

Structural studies on C-amidated amino acids and peptides: function of amide group in molecular association in crystal structures of Val-Gly-NH2, Ser-Phe-NH2, Gly-Tyr-NH2 and Pro-Tyr-NH2 hydrochloride salts.

As part of a series of elucidation of the structural features of peptides caused by C-terminal alpha-amidation, the crystal structures of H-Val-Gly-NH2, H-Ser-Phe-NH2, H-Gly-Tyr-NH2, and H-Pro-Tyr-NH2 hydrochloride salts were analyzed by the X-ray diffraction method. Although respective molecules take energetically allowable torsion angles concerning the backbone and side chains, their conformations are not necessarily the same as the corresponding unamidated ones. This results from the different molecular packing requirements, rather than from different conformational features inherent in the C-amidated and -unamidated peptides. As for the molecular packing feature, each peptide tended to form a repeated structure through those hydrogen bonds in which both amide NH and O=C groups participate. The chloride ions are located between the neighboring peptides and are hydrogen-bonded to the respective amide NHs, leading to the sheet structure. The hydrogen-bonding feature of the amide group and its function in molecular packing was discussed based on the results analyzed so far.

Amides↗

PubMed1987

FMRF-amide-like immunoreactive efferent fibers and FMRF-amide suppression of pacemaker neurons in eyes of Bulla.

The eyes of certain marine gastropods including Aplysia and Bulla, contain circadian pacemakers, which produce a circadian rhythm of autogenous compound action potential (CAP) activity. The CAPs are generated by the synchronous spike discharge of a distinctive population of retinal pacemaker neurons whose axons convey the CAP activity to the CNS. When CAP activity is recorded from a preparation with eyes attached to the CNS, the CAP activity is modulated by efferent activity. In this study we have identified FMRF-amide-like immunoreactive efferent axons in the optic nerves of Bulla. These axons arborize in the basal retinal neuropil adjacent to the pacemaker neurons and are in a position to make synaptic contacts with their dendrites. Similar immunoreactive fibers are not observed in Aplysia eyes. Exogenous FMRF-amide at micromolar concentrations suppresses ongoing CAP activity in isolated eyes but does not suppress the ERG or phase shift the circadian rhythm of CAP activity. Intracellular recordings from the retinal pacemaker neurons reveal that FMRF-amide hyperpolarizes the membrane potential, suppresses spike discharge, and decreases the input resistance, suggesting that a K conductance is increased. Electrical stimulation of the region of the cerebral ganglion that contains FMRF-amide immunoreactive neurons suppresses ongoing CAP activity. All these results are consistent with the idea that the FMRF-amide immunoreactive central neurons and their axons provide a pathway for efferent modulation of the CAP rhythm generated by the retinal pacemaker neurons.

Animals↗

PubMed1997

Exendin-4 agonist and exendin(9-39)amide antagonist of the GLP-1(7-36)amide effects in liver and muscle.

The GLP-1 structurally related peptides exendin-4 and exendin(9-39)amide were found to act, in rat liver and skeletal muscle, as agonist and antagonist, respectively, of the GLP-1(7-36)amide effects on glucose metabolism. Thus, like GLP-1(7-36)amide, exendin-4 increased glycogen synthase a activity and glucose incorporation into glycogen in both tissues and also stimulated exogenous D-glucose utilization and oxidation in muscle. These effects of GLP-1(7-36)amide and exendin-4 were inhibited by exendin(9-39)amide. Our findings provide further support to the proposed use of GLP-1, or exendin-4, as a tool in the treatment of diabetes mellitus. Thus, in addition to the well-known insulinotropic action of the peptides, they act both in liver and in muscle in a manner most suitable for restoration of glucose homeostasis, with emphasis on their positive effects upon glycogen synthesis in the two tissues and on the stimulation of exogenous glucose catabolism in muscle.

Animals↗

PubMed1990

The effects of two FMRFamide related peptides (A-18-F-amide and F-8-F-amide; 'morphine modulating peptides') on the endocrine and exocrine rat pancreas.

The effects of two recently isolated mammalian FMRFamide related peptides (A-18-F-amide and F-8-F-amide) on the encocrine and exocrine rat pancreas were investigated. A-18-F-amide (10, 100, 1000 pM) inhibited concentration dependently glucose (10 mM)- and arginine (10 mM)-induced insulin secretion from the isolated perfused rat pancreas during the first (controls: 100%; 10 pM: 114%; 100 pM: 63%, p less than 0.05; 1000 pM: 31%, p less than 0.05) and the second secretion phase (controls: 100%; 10 pM: 102%; 100 pM: 78%; 1000 pM: 27%, p less than 0.05). The inhibitory actions of A-18-F-amide on pancreatic D-cell secretion were more pronounced during the first than the second phase (first phase: controls: 100%; 10 pM: 95%; 100 pM: 37%, p less than 0.05; 1000 pM: 39%, p less than 0.05%; second phase: controls: 100%; 10 pM: 113%; 100 pM: 72%; 1000 pM: 59%, p less than 0.05). F-8-F-amide (at 1000 pM) inhibited stimulated insulin (controls: 100%; first phase: 26%, p less than 0.05%; second phase: 20%, p less than 0.05) and somatostatin release (controls: 100%; first phase: 14%, p less than 0.05; second phase: 29%, p less than 0.05). Both peptides were without effect on basal and CCK-8-stimulated amylase release from isolated incubated rat pancreatic acini.

Amino Acid Sequence↗

PubMed1998

Amidated and non-amidated glucagon-like peptide-1 (GLP-1): non-pancreatic effects (cephalic phase acid secretion) and stability in plasma in humans.

The incretin and enterogastrone hormone, GLP-1, occurs in an amidated (GLP-1 (7-36) amide; 75%) and a glycine-extended (GLP-1 (7-37); 25%) form. Their effects on the endocrine pancreas are similar and their overall (mainly renal) elimination rates appear to equal. Assuming that they might differentially affect non-pancreatic targets we investigated the effect of GLP-1 (7-37) infused at 0.7 pmol/kg/min on sham-feeding induced acid secretion in six healthy volunteers. The infusion increased the plasma concentrations from 16+/-2 pmol/l to 45+/-2 pmol/l. This was associated with a 61+/-14% decrease in acid output compared to saline and was not significantly different from that previously observed with GLP-1 (7-36) amide infused at the same rate. We then compared the degradation of the two forms in human plasma at 37 degrees C in vitro. T1/2 values were 32+/-3 (7-37) and 42+/-2 min (7-36) amide (P=0.007). The difference in metabolism persisted after addition of diprotin A, an inhibitor of dipeptidyl peptidase IV, the enzyme responsible for the initial degradation of GLP-1 in plasma, and broader enzyme inhibitors. Thus, the only effect of the amidation of GLP-1 seems to be to enhance its survival in plasma.

Adult↗

PubMed2004

A contrivance for a dynamic porous framework: cooperative guest adsorption based on square grids connected by amide-amide hydrogen bonds.

Flexible porous coordination polymers containing amide groups as a function origin have been synthesized and categorized as "Coordination Polymer with Amide Groups". Bispyridyl ligands with a spacer of amide group afford two-dimensional (2-D) motifs with a deformed square grid, resulting in three-dimensional (3-D) frameworks of [Co(NO(3))(2)(3-pna)(2)](n)(1), [Co(Br)(2)(3-pna)(2)](n)(2), and [[Co(NCS)(2)(4-peia)(2)].4Me(2)CO](n)(3 subset 4Me(2)CO) (3-pna = N-3-pyridylnicotinamide, 4-peia = N-(2-pyridin-4-yl-ethyl)-isonicotinamide), where the 2-D motifs are bound by complementary hydrogen bond between the amide groups. In the case of the 3 subset 4Me(2)CO, the amide groups form a contrivance for a dynamic porous framework because of their relevant position and orientation in the mutual nearest neighboring motifs. Consequently, 3 subset 4Me(2)CO shows amorphous (nonporous)-to-crystal (porous) structural rearrangement in the Me(2)CO adsorption and desorption process, where the framework of the 2-D motif is maintained. The adsorption isotherm has threshold pressure (P(th)), a sort of gate pressure. The heat of Me(2)CO adsorption (DeltaH(ad) = -25 kJ/mol) is obtained from the temperature dependence of threshold pressure (P(th)), which is close to acetone vaporization enthalpy (DeltaH(vap) = 30.99 kJ/mol).

Journal Article↗

PubMed1992

Isolation and identification of two neutral thyrotropin releasing hormone-like peptides, pyroglutamylphenylalanineproline amide and pyroglutamylglutamineproline amide, from human seminal fluid.

Two tripeptide amides with stuctures similar to thyrotropin releasing hormone were isolated from human seminal fluid and their amino acid sequences determined. The peptides were purified by gel exclusion from Sephadex G50 and were detected by radioimmunoassay with thyrotropin releasing hormone antibody; in addition, N-terminally extended forms were demonstrated by radioimmunoassay after trypsin digestion. Further purification of the tripeptides was by chromatography on SP-Sephadex C25 and by high performance liquid chromatography on C18 Microbondapak using an HCl/acetonitrile gradient. After exclusion from mini-columns of SP-Sephadex C25 and DEAE-Sephadex A25, two neutral peptides were obtained in homogeneous form by high performance liquid chromatography with an HCl/methanol gradient. Amino acid analysis gave the following compositions: Glu, 0.74, Phe, 1.0, Pro, 1.0; and Glu, 1.72, Pro, 1.0. Both peptides possessed a blocked N terminus, but after opening the pyroglutamyl ring the sequences Glu-Phe-Pro and Glu-Glx-Pro were demonstrated. The chromatographic properties of the endogenous peptides were identical to the properties of the corresponding synthetic peptides. The structure of pGlu-Phe-Pro (where p-indicates pyro-) amide was confirmed by fast atom bombardment mass spectrometry. The presence in human semen of three structurally related peptides, pGlu-Phe-Pro amide, pGlu-Gln-Pro amide, and the previously reported pGlu-Glu-Pro amide (Cockle, S. M., Aitken, A., Beg, F., and Smyth, D. G. (1989) J. Biol. Chem. 264, 7788-7791), suggests that this series of peptides may have evolved to fulfil complementary biological roles.

Amino Acid Sequence↗

PubMed1996

Effect of alkyl substitution at the amide nitrogen on amide bond cleavage: electrospray ionization/surface-induced dissociation fragmentation of substance P and two alkylated analogs.

Doubly protonated substance P and two analogs alkylated at the ninth position was studied to determine the effect of N-alkylation of the amide nitrogen on the electrospray ionization/surface-induced dissociation (ESI/SID) fragmentation pattern. Thermal decomposition experiments and ab initio calculations were also used in conjunction with the ESI/SID experiments. The increase in relative abundances of the product ions resulting from the cleavage of the amide bond at the alkylation site (relative to the corresponding cleavage for substance P) can be explained by the increased basicity of the amide nitrogen in the context of the 'mobile proton' model. The relative abundances of singly charged b ions suggest a rearrangement of the amide hydrogen located N-terminal to the bond cleaved.

Alkylation↗

PubMed2001

Investigation of aromatic-backbone amide interactions in the model peptide acetyl-Phe-Gly-Gly-N-methyl amide using molecular dynamics simulations and protein database search.

Weakly polar interactions between the side-chain aromatic rings and hydrogens of backbone amides (Ar-HN) are found in unique conformational regions. To characterize these conformational regions and to elucidate factors that determine the conformation of the Ar-HN interactions, four 4-ns molecular dynamics simulations were performed using four different low-energy conformations obtained from simulated annealing and one extended conformation of the model tripeptide Ac-Phe-Gly-Gly-NH-CH(3) as starting structures. The Ar(i)-HN(i+1) interactions were 4 times more frequent than were Ar(i)-HN(i+2) interactions. Half of the conformations with Ar(i)-HN(i+2) interactions also contained an Ar(i)-HN(i+1) interaction. The solvent access surface area of the Phe side chain and of the amide groups of Phe1, Gly2, and Gly3 involved in Ar-HN interactions was significantly smaller than in residues not involved in such interactions. The number of hydrogen bonds between the solvent and Phe1, Gly2, and Gly3 amide groups was also lower in conformations with Ar-HN interactions. For each trajectory, structures that contained Ar(i)-HN(i), Ar(i)-HN(i+1), and Ar(i)-HN(i+2) interactions were clustered on the basis of similarity of selected torsion angles. Attraction energies between the aromatic ring and the backbone amide in representative conformations of the clusters ranged from -1.98 to -9.24 kJ mol(-1) when an Ar-HN interaction was present. The most representative conformations from the largest clusters matched well with the conformations from the Protein Data Bank of Phe-Gly-Gly protein fragments containing Ar-HN interactions.

Amides↗

PubMed2002

Catalytic asymmetric epoxidation of alpha,beta-unsaturated amides: efficient synthesis of beta-aryl alpha-hydroxy amides using a one-pot tandem catalytic asymmetric epoxidation-Pd-catalyzed epoxide opening process.

The catalytic asymmetric epoxidation of alpha,beta-unsaturated amides using Sm-BINOL-Ph3As=O complex was succeeded. Using 5-10 mol % of the asymmetric catalyst, a variety of amides were epoxidized efficiently, yielding the corresponding alpha,beta-epoxy amides in up to 99% yield and in more than 99% ee. Moreover, the novel one-pot tandem process, one-pot tandem catalytic asymmetric epoxidation-Pd-catalyzed epoxide opening process, was developed. This method was successfully utilized for the efficient synthesis of beta-aryl alpha-hydroxy amides, including beta-aryllactyl-leucine methyl esters. Interestingly, it was found that beneficial modifications on the Pd catalyst were achieved by the constituents of the first epoxidation, producing a more suitable catalyst for the Pd-catalyzed epoxide opening reaction in terms of chemoselectivity.

Alcohols↗

PubMed2006

Organometallic chemistry of amidate complexes. accelerating effect of bidentate ligands on the reductive elimination of N-aryl amidates from palladium(II).

We report a series of arylpalladium complexes of acetamidate, sulfonamidate, and deprotonated oxazolidinone ligands that undergo reductive elimination with rates and yields that depend on the binding mode of the ancillary and amidate ligands. Complexes of the acetamidate ligands containing the bidentate phosphines DPPF and Xantphos as ancillary ligands undergo reductive elimination. The rate and yield were higher from the complex ligated by Xantphos, which contains a larger bite angle. In contrast, the analogous amidate complex containing a single sterically hindered monodentate ligand and a kappa2-bound amidate ligand does not undergo reductive elimination. This trend of faster reductive elimination from complexes containing bidentate ancillary ligands than from a complex with a single monodentate ancillary ligand is unusual and is consistent with an effect of the denticity of the ancillary ligand on the binding mode of the amidate. Complexes of sulfonamidate ligands underwent reductive elimination faster than complexes of acetamidates, and reductive elimination occurred from complexes containing both bidentate and monodentate ancillary ligands. Like reductive elimination from the acetamidate complexes, reductive eliminations from the sulfonamidate complexes were faster when the complexes possessed bidentate Xantphos and kappa1-sulfonamidate ligands.

Amides↗

PubMed1991

Amine prodrugs which utilize hydroxy amide lactonization. II. A potential esterase-sensitive amide prodrug.

In an effort to develop esterase-sensitive pro-prodrugs for amines, an amide derivative of 3-(2'-acetoxy-4',6'-dimethylphenyl)-3,3- dimethylpropionic acid (4-methoxyaniline amide 8) was synthesized and its stability investigated. This esterified hydroxy amide was found under all conditions to degrade via a two-step process initiated by acetyl ester hydrolysis generating the hydroxy amide intermediate 9a. The lactonization of this intermediate 9a in the second step resulted in the formation of 4-methoxyaniline (10) and 4,4,5,7-tetramethyl-3,4-dihydrocoumarin (1a). The pro-prodrug 8 was observed to possess the following half-lives at 37 degrees C under various conditions: 4030 min in phosphate buffer (50 mM, mu = 0.15) fixed to pH 7.4, 11.9 min in the same buffer containing a porcine liver esterase, 53.7 min in plasma, and 475 min in plasma containing diisopropylfluorophosphate. These results suggest that in a biological milieu the ester hydrolysis will occur by the enzymic hydrolysis rather than the chemical hydrolysis and that the enzymic hydrolysis of 8 in plasma is due, in part, to the action of serine-dependent esterases.

Amides↗

PubMed1990

Elucidation of amidating reaction mechanism by frog amidating enzyme, peptidylglycine alpha-hydroxylating monooxygenase, expressed in insect cell culture.

A frog 'peptidylglycine alpha-amidating monooxygenase (PAM, EC 1.14.17.3)' was expressed in cultured insect cells by using the baculovirus expression vector system. The enzyme, recovered in the culture medium, was purified to homogeneity. Its apparent molecular mass (43 kd), estimated by both SDS-PAGE and molecular sieving, was higher than the value (39 kd) for the 'PAM' (AE-I) purified from frog skin. N-terminal sequence analysis indicated that cleavage of signal sequence had occurred but the propeptide still remained at the N terminus. The glycine-extended model peptide X-Gly (mean = Ala-Ile-Gly-Val-Gly-Ala-Pro) was used as substrate for the purified enzyme. The reaction product formed at pH 5.4 was isolated and characterized by amino acid sequence analysis, FAB-MASS and 1H-NMR. It was shown that the purified enzyme had converted the model peptide to the C-terminal alpha-hydroxyglycine-extended peptide [X-Gly(OH)] instead of the amidated product (X-NH2), indicating that the enzyme widely known as 'PAM' should be called 'peptidylglycine alpha-hydroxylating monooxygenase'. A novel enzyme, present in the insect cell culture medium and separable from the expressed monooxygenase, could convert the alpha-hydroxyglycine-extended peptide to the amidated product at physiological pH values. It is concluded that the alpha-amidation of glycine-extended peptides is a two-step process catalyzed by the monooxygenase and the novel enzyme.

Amino Acid Sequence↗

PubMed1990

The 108-kDA peptidylglycine alpha-amidating monooxygenase precursor contains two separable enzymatic activities involved in peptide amidation.

A 43-kDa protein factor that increases the ability of purified bovine peptidylglycine alpha-amidating monooxygenase (PAM)-A and -B to produce alpha-amidated peptides at physiological pH was purified to homogeneity from bovine neurointermediate pituitary. At each step of the purification, the amount of activity correlated with the amount of protein detected on Western blots by antibody to bovine PAM(561-579). In the bovine neurointermediate pituitary the 108-kDa PAM precursor protein is cleaved to form a peptidylglycine alpha-hydroxylating monooxygenase and a peptidyl-alpha-hydroxyglycine alpha-amidating lyase, which function sequentially in the 2-step formation of alpha-amidated peptides.

Amidine-Lyases↗