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PubMed2006

Cooperative hydrogen bonding effects are key determinants of backbone amide proton chemical shifts in proteins.

A computational methodology for backbone amide proton chemical shift (delta(H)) predictions based on ab initio quantum mechanical treatment of part of the protein is presented. The method is used to predict and interpret 13 delta(H) values in protein G and ubiquitin. The predicted amide-amide delta(H) values are within 0.6 ppm of experiment, with a root-mean-square deviation (RMSD) of 0.3 ppm. We show that while the hydrogen bond geometry is the most important delta(H)-determinant, longer-range cooperative effects of extended hydrogen networks make significant contributions to delta(H). We present a simple model that accurately relates the protein structure to delta(H).

Amino Acid Sequence↗
PubMed2006

Quasi-isomeric gallium amides and imides GaNR2 and RGaNR (R = organic group): reactions of the digallene, Ar'GaGaAr' (Ar' = C6H3-2,6-(C6H3-2,6-Pri2)2) with unsaturated nitrogen compounds.

Reactions of the "digallene" Ar'GaGaAr'(1) (Ar' = C(6)H(3)-2,6-(C(6)H(3)-2,6-Pr(i)(2))(2)), which dissociates to green :GaAr' monomers in solution, with unsaturated N-N-bonded molecules are described. Treatment of solutions of :GaAr' with the bulky azide N(3)Ar(#) (Ar(#) = C(6)H(3)-2,6-(C(6)H(2)-2,6-Me(2)-4-Bu(t))(2)), afforded the red imide Ar'GaNAr(#) (2). Addition of the azobenzenes, ArylNNAryl (Aryl = C(6)H(4)-4-Me (p-tolyl), mesityl, and C(6)H(3)-2,6-Et(2)) yielded the 1,2-Ga(2)N(2) ring compound Ar'GaN(p-tolyl)N(p-tolyl)GaA' (3) or the products MesN=NC(6)H(2)-2,4-Me(2)-6-Ga(Me)Ar' (4) and 2,6-Et(2)C(6)H(3)N=NC(6)H(3)-2-Et-6-Ga(Et)Ar' (5). Reaction of GaAr' with N(2)CPh(2) yielded the 1,3-Ga(2)N(2) ring compound Ar'Ga(mu:eta(1)-N(2)CPh(2))(2)GaAr' (6), which is quasi-isomeric to 3. Calculations on simple model isomers showed that the Ga(I) amide GaNR(2) (R = Me) is much more stable than the isomeric Ga(III) imide RGaNR. This led to the synthesis of the first stable monomeric Ga(I) amide, GaN(SiMe(3))Ar' ' (8) (Ar' ' = C(6)H(3)-2,6-(C(6)H(2)-2,4,6-Me(3))(2) from the reaction of LiN(SiMe(3))Ar' ' (7) and "GaI". Compound 8 is also the first one-coordinate gallium species to be characterized in the solid state. The reaction of 8 with N(3)Ar' ' afforded the amido-imide derivative Ar' 'NGaN(SiMe(3))Ar' ' (9), a gallium nitrogen analogue of an allyl anion. All compounds were spectroscopically and structurally characterized. In addition, DFT calculations were performed on model compounds of the amide, imide, and cyclic 1,2- and 1,3-species to better understand their bonding. The pairs of compounds 2 and 8 as well as 3 and 6 are rare examples of quasi-isomeric heavier main group element compounds.

Journal Article↗
PubMed1994

Inhibition of peptidylglycine alpha-amidating monooxygenase by N-substituted homocysteine analogs.

C-terminal amidation is a posttranslational modification found in many neuropeptides. Peptidylglycine alpha-amidating monooxygenase (PAM) catalyzes the synthesis of the biologically essential C-terminal amide from a glycine-extended precursor peptide. Reported herein are the first potent inhibitors of PAM. Dipeptides containing a C-terminal homocysteine and an N-acylated hydrophobic amino acid were found to inhibit PAM with IC50s in the low nanomolar range. Inhibition potency was dependent on both the carboxylate and the thiolate functionalities of the homocysteine and on the hydrophobic groups of the second amino acid. The thiolate was postulated to produce high binding affinities through coordination with the active-site copper. The compound series also exhibited potent inhibition of PAM in rat dorsal root ganglion cells as demonstrated by a dose-dependent increase in the substance P-Gly/substance P ratio. These results indicate that the compounds have sufficient potency and intracellular bioavailability to aid future studies focused on neuropeptide function and the contributions of neuropeptides to various disease processes.

Animals↗
PubMed1993

A novel constrained reduced-amide inhibitor of HIV-1 protease derived from the sequential incorporation of gamma-turn mimetics into a model substrate.

C7 mimetics, designed to lock three amino acid residues of a peptide chain into a gamma-turn conformation, were introduced sequentially between the P3 to P2' positions of a model HIV-1 protease substrate I (resulting in compounds II-IV) to probe its conformational requirements in binding to HIV-1 protease. Of these, compound IIIa with the C7 mimetic replacing Asn-Tyr-Pro, corresponding to the P2 through P1' positions of substrate, was found to be an inhibitor with a Ki of 147 microM. Reduction of the amide bond in the C7 mimetic of IIIa resulted in a novel constrained reduced-amide mimetic VIa with a Ki of 430 nM. This corresponds to over a 300-fold improvement in inhibitory activity over the original C7 mimetic. The inhibitory activity of mimetic VIa was in addition found to be 44-fold better than a similar linear reduced-amide containing inhibitor V. The synthesis of these mimetics are described.

HIV Protease Inhibitors↗
PubMed1992

Stereoselective LSD-like activity in d-lysergic acid amides of (R)- and (S)-2-aminobutane.

The (R)- and (S)-2-butylamides of d-lysergic acid were prepared and evaluated in behavioral and biochemical assays of 5-HT2 agonist activity. In rats trained to discriminate 0.08 mg/kg LSD tartrate from saline, both isomers completely substituted for the training stimulus. Similarly, both isomers were found to possess very high affinity in displacing [125I]-(R)-DOI ([125I]-(R)-1-(2,5-dimethoxy-4-iodophenyl)-2- aminopropane) from rat cortical homogenate 5-HT2 receptors and in displacing [3H]-8-OH-DPAT ([3H]-8-hydroxy-2-(di-n-propylamino)tetralin) from rat hippocampal 5-HT1A receptors. The difference in activity between the two isomeric amides was significant in both the behavioral and binding assays, with the R isomer possessing greater potency. Molecular mechanics were used to predict the active geometries of the subject compounds. It was found that the (R)-2-butylamide has a conformation quite similar to LSD, while the (S)-2-butylamide does not. These results suggest that stereochemical properties of the amide substituent of hallucinogenic lysergamides may exert a critical influence on activity. It is concluded that the conformation of the amide function may directly affect binding through stereoselective interactions with a hydrophobic region on the receptor, indirectly by inducing conformational changes elsewhere in the molecule, or by a combination of these two mechanisms.

Animals↗
PubMed1992

Development of potent and selective CCK-A receptor agonists from Boc-CCK-4: tetrapeptides containing Lys(N epsilon)-amide residues.

A series of Boc-CCK-4 derivatives represented by the general structure Boc-Trp-Lys(N epsilon-COR)-Asp-Phe-NH2, where R is an aromatic, heterocyclic, or aliphatic group, are potent and selective CCK-A receptor agonists. These amide-bearing compounds complement the previously described urea-based tetrapeptides (Shiosaki et al. J. Med. Chem. 1991, 34, 2837-2842); structure-activity studies revealed parallel as well as divergent trends between these two series. A significant correlation was observed between pancreatic binding affinity and the resonance constant R of the phenyl substituent in one particular series of derivatives. Sulfation of phenolic amides appended onto the epsilon-amino group of the lysine did not affect affinity for the CCK-A receptor in contrast to the 500-fold increase in binding potency observed upon sulfation of CCK-8, suggesting that the lysine appendage and the sulfated tyrosine in CCK-8, both key structural elements that impart high affinity for the CCK-A receptor, are interacting differently with the receptor. The amide-bearing tetrapeptides are full agonists relative to CCK-8 in stimulating pancreatic amylase release while being partial agonists in eliciting phosphoinositide (PI) hydrolysis. Both effects were blocked by selective CCK-A receptor antagonists.

Amino Acid Sequence↗
PubMed1991

Synthesis and antihypertensive activity of pyran oxygen and amide nitrogen replacement analogues of the potassium channel activator cromakalim.

The synthesis and oral antihypertensive activity in conscious spontaneously hypertensive rats of two new series of compounds related to the prototype potassium channel activator cromakalim (1) are described. In the first series, replacement of the benzopyran oxygen atom by nitrogen or methylene led to the 1,2,3,4-tetrahydroquinoline 12 and 1,2,3,4-tetrahydronaphthalene 13, which were both less active than 1. However, in contrast to the equivalent activity found previously for 1 and its dehydrated analogue 28, the dihydronaphthalene 27 was found to be more active than 13. In the second series, replacement of the C(4) amide nitrogen atom in acyclic amides related to cromakalim by methylene gave ketone 16 that was less active than the corresponding amide 15. However, replacement of the 4-acetonyl substituent in 16 by N,N-dimethylacetamido as in compound 22 resulted in a marked enhancement in activity. The compounds described in this paper thus illustrate the importance of the benzopyran oxygen and C(4) substituent on antihypertensive activity in the cromakalim series of potassium channel activators.

Administration, Oral↗
PubMed1989

Synthesis, opioid receptor binding profile, and antinociceptive activity of 1-azaspiro[4.5]decan-10-yl amides.

A series of azaspiro[4.5]decanyl amides were prepared by a novel cyclization route and examined for opiate receptor binding and antinociceptive activity. Selected tertiary amides in this series showed potent selective mu-receptor binding and antinociceptive activity, in contrast to the less conformationally restricted secondary amides, which showed relatively weak activity. Although structurally similar to the kappa-agonist U-50488H (1), these compounds showed virtually no tendency to bind to the kappa-receptor. An X-ray crystal structure of compound (21) confirms that the spirocyclic amine does not cause distortion away from the chair conformation of the cyclohexane ring. Either this receptor has very specific requirements for the orientation of the two nitrogens of these compounds or this ring system fills a portion of space more readily tolerated by the mu- and delta-receptors.

Analgesia↗
PubMed1990

Functionalized congener approach for the design of novel muscarinic agents. Synthesis and pharmacological evaluation of N-methyl-N-[4-(1-pyrrolidinyl)-2-butynyl] amides.

A functionalized congener approach was used to design ligands for muscarinic cholinergic receptors (mAChRs). A series of omega-functionalized alkyl amides of N-methyl-4-(1-pyrrolidinyl)-2-butynamine (22) were prepared as functionalized analogues of UH 5 [N-methyl-N-[4-(1-pyrrolidinyl)-2-butynyl]acetamide], a muscarinic agonist related to oxotremorine. Intermediate 22 was coupled to a series of Boc-protected omega-amino acids, and the resulting amides were deprotected and acylated. Intermediate 22 was also acylated with succinic anhydride and derivatized. The synthetic intermediates and final compounds were evaluated in vitro for their effects on the turnover of phosphatidylinositides in SK-N-SH human neuroblastoma cells that express m3AChRs, and on the production of cyclic AMP in NG108-15 neuroblastoma x glioma cells that express only m4AChRs. The displacement of [3H]-N-methylscopolamine was also measured in membrane preparations from each of these cell lines. Conjugates of glycine and beta-alanine were agonists at m4AChRs, having little or no activity at m3AChRs. The potency in displacement of [3H]-N-methylscopolamine from both m3- and m4AChRs generally increased with increasing chain lengths of the omega-aminoalkyl congeners. The amides of 7-aminoheptanoic acid and 8-aminooctanoic acid, and their Boc-protected derivatives, had comparable affinities to UH 5 (Ki = 5.0 and 4.5 microM at m3AChRs and at m4AChRs, respectively) at both receptors but lacked any agonist effects.

Alprostadil↗
PubMed1980

Thrombin inhibitors. 3. Carboxyl-containing amide derivatives of N alpha-substituted L-arginine.

A series of N alpha-(arylsulfonyl)-L-arginine amide derivatives having carboxamide N-substituents with a carboxyl group was prepared and tested as inhibitors of the clotting activity of thrombin. The most inhibitory compounds were obtained when a carboxyl group was introduced into the carbon next to the amide nitrogen of N alpha-(arylsulfonyl)-L-arginine amide derivatives, e.g., N alpha-(arylsulfonyl)-L-arginyl-N-butyl-, N-(methoxyethyl)- or N-(tetrahydrofurfuryl)glycine and 4-alkyl-1-[N alpha-(arylsulfonyl)-L-arginyl]-2-piperidinecarboxylic acid, with an I50 of 1-3 X 10(-7) M.

Animals↗
PubMed1982

Pyridazinones. 1. Synthesis and antisecretory and antiulcer activities of thio amide derivatives.

In an effort to develop new types of antiulcer agents, a series of novel 3(2H)-pyridazinone derivatives and related analogues was synthesized. Substituted 3(2H)-pyridazinones and their 4,5-dihydro analogues were alkylated by omega-haloalkyl cyanides at the N-2 position under phase-transfer catalytic reaction, and the nitrile group was converted to the thio amide group by treatment with hydrogen sulfide alone or with the appropriate primary or secondary amines. Various substituents were introduced on the nitrogen of thio amide, on the carbon in the side chains, and on the 3(2H)-pyridazinone ring. The synthesized compounds were evaluated for gastric antisecretory activity in the pylorus-ligated rat, and selected compounds were applied to experimental ulcer models, such as Shay's, aspirin-induced, and stress-induced ulcers in the rat. Structure-activity relationships are discussed. 3(2H)-Pyridazinones with a C-6 phenyl group and an N-2 alkyl side chain with a terminal thio amide group (48, 49, 51, and 52) were the most potent among the compounds tested.

Animals↗
PubMed1985

Bile acids with cyclopropane-containing side chain. 2. Synthesis and properties of 3 alpha,7 beta-dihydroxy-22,23-methylene-5 beta-cholan-24-oic acid (2-sulfoethyl)amide.

The preparation of 3 alpha,7 beta-dihydroxy-22,23-methylene-5 beta-cholan-24-oic acid (2-sulfoethyl)amide (5) by the one-step EEDQ-induced conjugation between ursodeoxycholic acid "cyclopropylog" (4) and taurine is described. The presence of a cyclopropyl ring adjacent to the amide bond is shown to make it resistant to degradation by intestinal bacteria. This new cyclopropylog is neither deconjugated at the C-24 amide bond nor 7-dehydroxylated when incubated with human stools in anaerobic conditions.

Anaerobiosis↗
PubMed2002

Synthesis and structure-activity relationships of amide and hydrazide analogues of the cannabinoid CB(1) receptor antagonist N-(piperidinyl)- 5-(4-chlorophenyl)-1-(2,4-dichlorophenyl)-4-methyl-1H-pyrazole-3-carboxamide (SR141716).

Analogues of the biaryl pyrazole N-(piperidinyl)-5-(4-chlorophenyl)-1-(2,4-dichlorophenyl)-4-methyl-1H-pyrazole-3-carboxamide (SR141716; 5) were synthesized to investigate the structure-activity relationship (SAR) of the aminopiperidine region. The structural modifications include the substitution of alkyl hydrazines, amines, and hydroxyalkylamines of varying lengths for the aminopiperidinyl moiety. Proximity and steric requirements at the aminopiperidine region were probed by the synthesis of analogues that substitute alkyl hydrazines of increasing chain length and branching. The corresponding amide analogues were compared to the hydrazides to determine the effect of the second nitrogen on receptor binding affinity. The N-cyclohexyl amide 14 represents a direct methine for nitrogen substitution for 5, reducing the potential for heteroatom interaction, while the morpholino analogue 15 adds the potential for an additional heteroatom interaction. The series of hydroxyalkyl amides of increasing chain length was synthesized to investigate the existence of additional receptor hydrogen binding sites. In displacement assays using the cannabinoid agonist [(3)H](1R,3R,4R)-3-[2-hydroxy-4-(1,1-dimethylheptyl)phenyl]-4-(3-hydroxypropyl) cyclohexan-1-ol (CP 55 940; 2) or the antagonist [(3)H]5, 14 exhibited the highest CB(1) affinity. In general, increasing the length and bulk of the substituent was associated with increased receptor affinity and efficacy (as measured in a guanosine 5'-triphosphate-gamma-[(35)S] assay). However, in most instances, receptor affinity and efficacy increases were no longer observed after a certain chain length was reached. A quantitative SAR study was carried out to characterize the pharmacophoric requirements of the aminopiperidine region. This model indicates that ligands that exceed 3 A in length would have reduced potency and affinity with respect to 5 and that substituents with a positive charge density in the aminopiperidine region would be predicted to possess increased pharmacological activity.

Animals↗
PubMed1996

Novel peptidyl alpha-keto amide inhibitors of calpains and other cysteine proteases.

A series of new dipeptidyl alpha-keto amides of the general structure R1-L-Leu-D,L-AA-CONH-R2 were synthesized and evaluated as inhibitors for the cysteine proteases calpain I, calpain II, and cathepsin B. They combine 10 different N-protecting groups (R1), 3 amino acids residues in P1 (AA), and 44 distinct substituents on the alpha-keto amide nitrogen (R2). In general, calpain II was more sensitive to these inhibitors than calpain I, with a large number of inhibitors displaying dissociation constants (Ki) in the 10-100 nM range. Calpain I was also effectively inhibited, but very low Ki values were observed with a smaller number of inhibitors than with calpain II. Cathepsin B was weakly inhibited by most compounds in this study. The best inhibitors for calpain II were Z-Leu-Abu-CONH-CH2-CHOH-C6H5 (Ki = 15 nM), Z-Leu-Abu-CONH-CH2-2-pyridyl (Ki = 17 nM), and Z-Leu-Abu-CONH-CH2-C6H3(3,5(OMe)2) (Ki = 22 nM). The best calpain I inhibitor in this study was Z-Leu-Nva-CONH-CH2-2-pyridyl (Ki = 19 nM). The peptide alpha-keto amide Z-Leu-Abu-CONH-(CH2)2-3-indolyl was the best inhibitor for cathepsin B (Ki = 31 nM). Some compounds acted as specific calpain inhibitors, with comparable activity on both calpains I and II and a lack of activity on cathepsin B (e.g., 40, 42, 48, 70). Others were specific inhibitors for calpain I (e.g., 73) or calpain II (e.g., 18, 19, 33, 35, 56). Such inhibitors may be useful in elucidating the physiological and pathological events involving these proteases and may become possible therapeutic agents.

Animals↗
PubMed2001

A mild and general solid-phase method for the synthesis of chiral polyamines. Solution studies on the cleavage of borane-amine intermediates from the reduction of secondary amides.

A mild oxidative workup protocol using iodine in an acetic acid-acetate buffer solution is described for the cleavage of borane-amine adducts arising from the borane-promoted reduction of polyamides supported onto practical trityl-based resins. Chiral polyamines with diverse side-chain functionalities can be generated as free bases without premature release from the solid support and with essentially no racemization using this method. A series of model oligomeric secondary diamides 6 containing various alpha-amino acid residues (Val, Phe, Tyr, Ser, Cys, Met, Gln, Trp) provided triamine products 8 in high yields and good to excellent purity. On the other hand, a substrate containing a tertiary amide (15) formed a rather unusual triaminoborane intermediate that required more stringent workup conditions to liberate the polyamine product 20. The reduction of oligomeric tertiary amides such as 9 was found sluggish, but these compounds could nonetheless be obtained in high purity from in situ reductive amination of the corresponding secondary amines. Control studies, carried out in solution with model secondary amide 23, confirmed the efficiency of the buffered iodine solution and highlighted several advantages (no heating necessary, no need for strong bases or acids) over existing methods for the cleavage of borane-amine adducts. A possible mechanism involving all buffer components (iodine, acetic acid, and acetate ion) is proposed in which borane-amine adducts are transformed first to the monoiodoborane-amine and then to the corresponding acetoxyborane-amine adduct of much weaker coordination affinity. The latter would dissociate readily and get trapped by the acetic acid to provide the desired secondary amine. This reduction/oxidative workup protocol is useful as a general method for the facile solid-phase synthesis of polyamines for eventual release in solution and use in various applications. It is also potentially very useful toward the synthesis and screening of bead-supported libraries of free oligoamines assembled through split-pool methods.

Journal Article↗
PubMed2001

Bis-2-oxo amide triacylglycerol analogues: a novel class of potent human gastric lipase inhibitors.

A novel class of potent human gastric lipase inhibitors, bis-2-oxo amide triacylglycerol analogues, was developed. These analogues of the natural substrate of lipases were prepared starting from 1,3-diaminopropan-2-ol. They were designed to contain the 2-oxo amide functionality in place of the scissile ester bond at the sn-1 and sn-3 position, while the ester bond at the sn-2 position was either maintained or replaced by an ether bond. The derivatives synthesized were tested for their ability to form stable monomolecular films at the air/water interface by recording their surface pressure/molecular area compression isotherms. The inhibition of human pancreatic and gastric lipases by the bis-2-oxo amides was studied using the monolayer technique with mixed films of 1,2-dicaprin containing variable proportions of each inhibitor. The nature of the functional group (ester or ether), as well as the chain length, at the sn-2 position influenced the potency of the inhibition. Among the compounds tested, 2-[(2-oxohexadecanoyl)amino]-1-[[(2-oxohexadecanoyl)-amino]methyl]ethyl decanoate was the most potent inhibitor, causing a 50% decrease in HPL and HGL activities at 0.076 and 0.020 surface molar fractions, respectively.

Enzyme Inhibitors↗
PubMed2002

Conformational studies by dynamic NMR. 88.(1) stereomutation processes in the diastereoisomers of a representative amino alcohol and related amide precursors.

The barriers for three internal motions (i.e., phenyl and tert-butyl rotation as well as N-inversion) have been determined by dynamic NMR spectroscopy in the two diastereoisomeric forms of a typical amino alcohol [dimethylamino-2,4,4-trimethyl-3-phenyl-3-pentanol, Me(2)NCH(2)CHMeC(OH)PhBu(t)]. The two structures were assigned by connection with those of the corresponding amide precursors determined by single-crystal X-ray diffraction. These amides (C=O in place of CH(2)) too were found to undertake internal motions amenable to NMR observation, i.e., phenyl, tert-butyl, and N-CO rotations: the corresponding barriers were also measured. Ab initio computations indicate that H-bonding makes all these molecules adopt six-membered cyclic conformations, a conclusion which agrees well with the X-ray crystal structure determined for the amide precursors.

Journal Article↗
PubMed2004

Intramolecular C-N bond formation reactions catalyzed by ruthenium porphyrins: amidation of sulfamate esters and aziridination of unsaturated sulfonamides.

Ruthenium porphyrins [Ru(F(20)-TPP)(CO)] (F(20)-TPP = 5,10,15,20-tetrakis(pentafluorophenyl)porphyrinato dianion) and [Ru(Por*)(CO)] (Por = 5,10,15,20-tetrakis[(1S,4R,5R,8S)-1,2,3,4,5,6,7,8-octahydro-1,4:5,8-dimethanoanthracen-9-yl]porphyrinato dianion) catalyzed intramolecular amidation of sulfamate esters p-X-C(6)H(4)(CH(2))(2)OSO(2)NH(2) (X = Cl, Me, MeO), XC(6)H(4)(CH(2))(3)OSO(2)NH(2) (X = p-F, p-MeO, m-MeO), and Ar(CH(2))(2)OSO(2)NH(2) (Ar = naphthalen-1-yl, naphthalen-2-yl) with PhI(OAc)(2) to afford the corresponding cyclic sulfamidates in up to 89% yield with up to 100% substrate conversion; up to 88% ee was attained in the asymmetric intramolecular amidation catalyzed by [Ru(Por)(CO)]. Reaction of [Ru(F(20)-TPP)(CO)] with PhI[double bond]NSO(2)OCH(2)CCl(3) (prepared by treating the sulfamate ester Cl(3)CCH(2)OSO(2)NH(2) with PhI(OAc)(2)) afforded a bis(imido)ruthenium(VI) porphyrin, [Ru(VI)(F(20)-TPP)(NSO(2)OCH(2)CCl(3))(2)], in 60% yield. A mechanism involving reactive imido ruthenium porphyrin intermediate was proposed for the ruthenium porphyrin-catalyzed intramolecular amidation of sulfamate esters. Complex [Ru(F(20)-TPP)(CO)] is an active catalyst for intramolecular aziridination of unsaturated sulfonamides with PhI(OAc)(2), producing corresponding bicyclic aziridines in up to 87% yield with up to 100% substrate conversion and high turnover (up to 2014).

Journal Article↗