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PubMed2001

1-Alkyl-3-amino-5-aryl-1H-[1,2,4]triazoles: novel synthesis via cyclization of N-acyl-S-methylisothioureas with alkylhydrazines and their potent corticotropin-releasing factor-1 (CRF(1)) receptor antagonist activities.

Cyclizations of alkylhydrazines with N-acyl-S-methylisothioureas, readily synthesized from acyl chlorides, sodium thioisocyanate, dialkylamines then methyl iodide in a one-pot reaction, gave 1-alkyl-3-dialkylamino-5-phenyltriazoles 7 as major products. The regioisomers were assigned through the use of NOE NMR experiments. While bearing a N-bis(cyclopropyl)methyl-N-propylamino group, this series of compounds shows very good binding affinity on the human CRF(1) receptor. Among them, 1-methyl-3-[N-bis(cyclopropyl)methyl-N-propylamino]-5-(2,4-dichlorophenyl)-1H-[1,2,4]triazole 7a had the best binding affinity for the CRF(1) receptor (K(i)=9 nM).

Humans↗

PubMed1999

Potent, orally bioavailable somatostatin agonists: good absorption achieved by urea backbone cyclization.

Backbone cyclization of urea-based somatostatin agonists resulted in novel, orally bioavailable agonists. Binding assays confirmed that the resulting conformationally constrained cyclic ureas retained the potency of their acyclic counterparts. SAR studies subsequently led to highly potent analogs, selective for receptor subtype 2, and having good oral bioavailability.

Administration, Oral↗

PubMed2001

Cyclization of ortho-cyclopropylphenyl benzamides in gas and liquid phases.

The electron ionization (EI) and collision-induced dissociation (CID) spectra of substituted N-(ortho-cyclopropylphenyl)benzamides 1-7 and N-[ortho-(1-methylcyclopropyl)phenyl]benzamides 8-12 were recorded. In addition to routine bond cleavages, the molecular ions (M+) of 1-12 undergo cyclization into the corresponding 3-aryl-1-alkyl-1-ethyl-1H-benzoxazines and isomeric 5-ethyl-2-oxodibenzoazepines. The presence of a methyl group in the cyclopropyl ring (compounds 8-12) makes the formation of 5-ethyl-2-oxodibenzoazepine less favorable. In accord with mass spectrometric predictions, compound 13 (3-p-tolyl-1-ethyl-1H-benzoxazine) was obtained as a major product of the reaction of N-(ortho-cyclopropylphenyl)-4-methylbenzamide 1 with sulfuric acid. Traces of 5-ethyl-2-oxodibenzoazepine were also detected in gas chromatography-mass spectrometry (GC-MS) analysis of the reaction mixture although the yield was too low to allow its isolation.

Journal Article↗

PubMed1983

Fate of an intervening sequence ribonucleic acid: excision and cyclization of the Tetrahymena ribosomal ribonucleic acid intervening sequence in vivo.

In previous studies of RNA splicing in vitro, we have shown that the intervening sequence (IVS) of the Tetrahymena rRNA precursor is excised as a unique linear RNA molecule and subsequently cyclized. In the present work, we have investigated the occurrence and stability of these RNA species in vivo. RNA was separated by gel electrophoresis, transferred to diazotized paper, and hybridized with 32P-labeled DNA probes. RNA molecules containing the IVS were found to reside within the nucleus and not in the cytoplasm. The species found in nucleus include both the linear and circular forms of the excised IVS RNA, as well as the unspliced precursor. On the basis of quantitation of the hybridization, the half-lives of the IVS-containing pre-rRNA and the excised IVS RNA in rapidly growing cells were estimated as 2 and 6 s, respectively. We conclude that splicing is not a rate-limiting step in rRNA maturation and that the IVS RNA is quickly degraded after its excision. When the deproteinized nuclear RNA was incubated at 37 degrees C in a Mg2+-containing solution, a substantial portion of the linear IVS RNA was converted to the circular form. Autocyclization, previously characterized with IVS RNA produced by splicing in vitro, is therefore also a property of IVS RNA produced in vivo.

Animals↗

PubMed1990

Melting and chemical modification of a cyclized self-splicing group I intron: similarity of structures in 1 M Na+, in 10 mM Mg2+, and in the presence of substrate.

C IVS is the cyclized form of the intron from the RNA precursor of the Tetrahymena thermophila large subunit (LSU) ribosomal RNA. C IVS was mapped by chemical modification in 1 M Na+, 0.05 M Na+ and 10 mM Mg2+ (Na+/Mg2+), and Na+/Mg2+ with CUCU substrate. The results suggest the secondary structure is similar for all three conditions. Optical melting curves were also measured for C IVS in 1 M Na+ and Na+/Mg2+ and indicate the secondary structures have similar stabilities under both conditions. Computer predictions of secondary structure and stability are in good agreement with observations. The results suggest that many of the approximations used for computer prediction of secondary structure by free energy minimization are reasonable.

Aldehydes↗

PubMed1979

Proton nuclear magnetic resonance study of the conformation and configuration of the cyclized pyridine nucleotide adducts.

We have closely examined by high-frequenty 1H nuclear magnetic resonance spectroscopy the structure of the adducts which form when various carbonyl compounds react with pyridine nucleotides at elevated pH. These studies show that the adducts of N-(2,6-dichlorobenzyl)nicotinamide-acetone, n-(2,6-dichlorobenzyl)nicotinamide-pyruvate, NMN-pyruvate, NAD-pyruvate, NAD-acetaldehyde, and NAD-oxaloacetate form with identical structural features as well as configuration. The following structural features are observed: (1) the adducts are pyridine N-4-substituted compounds; (2) a second six-membered ring forms by addition of the nicotinamide amido to the carbonyl group of the compound forming the addition complex; (3) cyclization occurs stereospecifically, indicating that the stereochemistry is predetermined by the initial attack at the N-4 position; (4) two diastereomeric forms are observed for each nucleotide adduct. Finally, the determination of configuration at all symmetric carbon atoms in these adducts will be discussed.

Acetaldehyde↗

PubMed2001

Purification, characterization, and substrate and inhibitor structure-activity studies of rat liver FAD-AMP lyase (cyclizing): preference for FAD and specificity for splitting ribonucleoside diphosphate-X into ribonucleotide and a five-atom cyclic phosphodiester of X, either a monocyclic compound or a cis-bicyclic phosphodiester-pyranose fusion.

An enzyme with FAD-AMP lyase (cyclizing) activity, splitting FAD to AMP and riboflavin 4',5'-phosphate (cFMN), was recently identified [Fraiz, F., et al. (1998) Biochem. J. 330, 881-888]. Now, it has been purified to apparent homogeneity from a rat liver supernatant, by a procedure that includes affinity for ADP-agarose (adsorption required the activating cation Mn2+ and desorption required its removal), to a final activity of 2.2 units/mg after a 240-fold purification with a 15% yield. By SDS-PAGE, only one protein band was observed (Mr = 59 000). The correspondence between protein and enzyme activity was demonstrated by renaturation after SDS-PAGE, by gradient ultracentrifugation followed by analytical SDS-PAGE, and by native PAGE with visualization of enzyme activity by fluorescence. A native Mr of 100 000 (ultracentrifugation) or 140 000 (gel filtration) indicated that FAD-AMP lyase could be a dimer. The enzyme required millimolar concentrations of Mn2+ or Co2+, exhibited different optimum pH values with these cations (pH 8.5 or 7.3, respectively), and was strongly inhibited by ADP or ATP, but not by dADP, dATP, or the reaction products AMP and cFMN. A specificity study was conducted with 35 compounds related to FAD, mostly nucleoside diphosphate-X (NDP-X) derivatives. Besides FAD, the enzyme split 11 of these compounds with the pattern NDP-X --> NMP + P=X. Structure-activity correlations of substrates, nonsubstrates, and inhibitors, and the comparison of the enzymic reactivities of NDP-X compounds with their susceptibilities to metal-dependent chemical degradation, pinpointed the following specificity pattern. FAD-AMP lyase splits ribonucleoside diphosphate-X compounds in which X is an acyclic or cyclic monosaccharide or derivative bearing an X-OH group that is able to attack internally the proximal phosphorus with the geometry necessary to form a P=X product, either a five-atom monocyclic phosphodiester or a cis-bicyclic phosphodiester-pyranose fusion. For instance, NDP-glucose and GDP-alpha-L-fucose were substrates, but dTDP-glucose, NDP-mannose, and GDP-beta-L-fucose were not. Judging from kcat/Km ratios, we found the best substrate to be FAD, followed closely by ADP-glucose (kcat/Km only 2-fold lower, but not a physiological compound in mammals), whereas other substrates exhibited 50-500-fold lower kcat/Km values. However, there was no evidence for specific flavin recognition. Instead, what seems to be recognized is the NDP moiety of NDP-X, with a strong preference for ADP-X. Splitting would then depend on the presence of an adequate X-OH group. The possibility that, besides FAD, there could be in mammals other ADP-X substrates of FAD-AMP lyase is discussed, with emphasis placed on some ADP-ribose derivatives.

Adenosine Diphosphate↗

PubMed2004

Traditional GFP-type cyclization and unexpected fragmentation site in a purple chromoprotein from Anemonia sulcata, asFP595.

The purple chromoprotein (asFP595) from Anemonia sulcata belongs to the family of green fluorescent protein (GFP). Absorption and emission spectra of asFP595 are similar to those of a number of recently cloned GFP-like red proteins of the DsRed subfamily. The earlier proposed asFP595 chromophore structure [Martynov, V. I.; et al. (2001) J. Biol. Chem. 276, 21012-21016] was postulated to result from an "alternative cyclization" giving rise to a pyrazine-type six-membered heterocycle. Here we report that the asFP595 chromophore is actually very close in chemical structure to that of zFP538, a yellow fluorescent protein [Zagranichny, V. E.; et al. (2004) Biochemistry 43, 4764-4772]. NMR spectroscopic studies of four chromophore-containing peptides (chromopeptides) isolated under mild conditions from enzymatic digests of asFP595 and one chromopeptide obtained from DsRed revealed that all of them contain a p-hydroxybenzylideneimidazolinone moiety formed by Met-65/Gln-66, Tyr-66/67, and Gly-67/68 of asFP595/DsRed, respectively. Two asFP595 chromopeptides are proteolysis products of an isolated full-length polypeptide containing a GFP-type chromophore already formed and arrested at an earlier stage of maturation. The two other asFP595 chromopeptides were isolated as proteolysis products of the purified chromophore-containing C-terminal fragment. One of these has an oxo group at Met-65 C(alpha) and is a hydrolysis product of another one, with the imino group at Met-65 C(alpha). The N-unsubstituted imino moiety of the latter is generated by spontaneous polypeptide chain cleavage at a very unexpected site, the former peptide bond between Cys-64 C' and Met-65 N(alpha). Our data strongly suggest that both zFP538 and asFP595 could be attributed to the DsRed subfamily of GFP-like proteins.

Animals↗

PubMed1996

Structural distortions induced by integration host factor (IHF) at the H' site of phage lambda probed by (+)-CC-1065, pluramycin, and KMnO4 and by DNA cyclization studies.

Integration Host Factor (IHF) is a sequence-specific DNA-bending protein that is proposed to interact with DNA primarily through the minor groove. We have used various chemical probes [(+)-CC-1065, a minor-groove-specific agent that alkylates N3 of adenine and traps bends into the minor groove; pluramycin, a minor-major-groove threading intercalator that alkylates N7 of guanine; KMnO4, which reacts more strongly with bases in denatured DNA] to gain more information on the interaction of IHF with the H' site of phage lambda. In addition to the 13-bp core consensus recognition element present at all IHF binding sites, the H' site also has an upstream AT-rich element that increases the affinity of IHF for this site. Our results reveal new details of IHF-DNA interaction at this site. Results with (+)-CC-1065 modification suggest that IHF interacts with the adenines on the 3'-side of the AT-rich element and likely induces a minor-groove bend in its vicinity, which in turn stabilizes the interaction. Pluramycin modification experiments suggest the presence of both short- and long-range structural perturbations (possible DNA unwinding events) on either side of the IHF contact region. Although IHF is known to induce a large bend in DNA at the H' site, no separation of base pairs was detected when the bent DNA was probed with KMnO4. DNA cyclization studies indicate a large magnitude (approximately 180 degrees) for the IHF-induced bend at the H' site, consistent with > 140 degrees bend estimated by gel electrophoresis methods. These studies suggest that IHF-induced DNA bending is accompanied by the introduction of a DNA node, DNA unwinding, and/or by some other DNA distortion. An enhanced binding and stability of IHF was observed on small circular DNA.

Adenine↗

PubMed1999

Cyclization of globular DNA. Implications for DNA-DNA interactions in vivo.

The rate of cyclization of lambda DNA varies over more than 6 orders of magnitude, from 3.2 x 10(-7) s-1 to 2 s-1, in a Tris-EDTA buffer as a function of spermidine concentration. This variation is strictly correlated with the conformation of the chain. The highest rates are obtained when the chain is collapsed into a dense globular state. The effective concentration of the chain ends in the reaction is then 87 000-fold greater than in the random coil state. These results show that DNA globularity must be taken into account to understand biological processes involving intramolecular DNA-DNA interactions.

Bacteriophage lambda↗

PubMed2002

Oxovanadium(V) and cobalt(III) complexes of dithiocarbazate-based Schiff base ligands: formation of a thiadiazole ring by vanadium-induced cyclization of the coordinated ligand.

S-Methyl 3-((2-hydroxyphenyl)methyl)dithiocarbazate (H(2)L(1)) and its bromo derivative (H(2)L(2)), which are traditionally biprotic tridentate (ONS) ligands, behave in an unprecedented manner when allowed to react with [VO(acac)(2)] under an oxidative environment in acetonitrile-water medium containing a catalytic amount of alkali metal ion. The products obtained are oxovanadium(V) compounds [VOL(L(cyclic))] (L = L(1), 1a, and L(2), 1b) that contain one molecule of ligand which undergoes metal-induced cyclization to form a thiadiazole ring. Compound 1a crystallizes in the triclinic space group P(-)1 with a = 9.1830(9) A, b = 9.4165(12) A, c = 12.700(2) A, alpha = 100.988(8)(o), beta = 100.195(7)(o), gamma = 78.774(8)(o), V = 1046.3(2) A(3), and Z = 2. With cobalt(III), however, the products [CoL(HL)].H(2)O (L = L(1), 2a, and L(2), 2b) have hydrogen-bonded dimeric structures with each ligand virtually carrying 1.5 units of negative charge as confirmed by X-ray crystal structure analysis of 2a. It also crystallizes in triclinic space group P(-)1 with a = 12.0842(8) A, b = 13.5251(9) A, c = 14.1960(10) A, alpha = 78.122(6)(o), beta = 73.888(6)(o), gamma = 78.255(6)(o), V = 2154.7(3) A(3), and Z = 4. In solution, 2a is a symmetric molecule as indicated by (1)H NMR, involving a characteristic hydrogen-bonded O-H-O broad feature in the downfield (at 14.5 ppm) connecting both monoprotonated (LH(-)) and deprotonated (L(2-)) forms of the ligand--a situation somewhat analogous to the classic H-F-H case as observed in bifluoride ion.

Journal Article↗

PubMed2005

Extending the nitrogen-heterosuperbenzene family: the spectroscopic, redox, and photophysical properties of "half-cyclized" N-1/2HSB and Its Ru(II) complex.

Oxidative cyclodehydrogenation is an important process in the formation of the new graphene, N-(1)/(2)HSB 2. This heteropolyaromatic results from the FeCl(3)-catalyzed oxidative cyclodehydrogenation of 1,2-dipyrimidyl-3,4,5,6-tetra-(4-tert-butylphenyl)benzene. Three new C-C bonds are formed that lock the two pyrimidines in a molecular platform comprising eight fused aromatic rings flanked by two remaining "uncyclized" phenyl rings. Mechanistically intriguing is the fact that N-HSB 1, the product of six C-C bond fusions, is co-synthesized with its "half-cyclized" daughter in this reaction. 1 and 2 have the same bidentate N-atom arrangement. This facilitates formation of the heteroleptic Ru(II) complexes, [Ru(bpy)(2)(2)](PF(6))(2) 4 and [Ru(bpy)(2)(1)](PF(6))(2) 3, which differ in the size and planarity of their aromatic ligands. The new ligand 2 and its complex 4 are characterized by (1)H NMR, IR, ESI-MS, and accurate mass methods. 2 exhibits photophysical properties that are consistent with a reduction of the pi/pi framework, a concomitant increase in the energy of the LUMO, and a blue-shift of the solvent-dependent fluorescence (lambda(em) = 474 nm, phi(F) = 0.55, toluene) as compared to its parent. Complex 4 absorbs throughout the visible region and borders on near-IR emitter character, exhibiting a slightly blue-shifted (3)MLCT emission (868 nm, CH(3)CN) as compared to that of [Ru(bpy)(2)(1)](PF(6))(2) 3 (880 nm, CH(3)CN). Electrochemical analyses permit further elucidation of the intermolecular interactions of 3 and 4. These and the concentration and temperature-dependent NMR spectra of 4 confirm it to be nonaggregating, a direct result of the two uncyclized and rotatable phenyl rings in 2.

Journal Article↗

PubMed2001

A minimal peptide scaffold for beta-turn display: optimizing a strand position in disulfide-cyclized beta-hairpins.

Phage display of peptide libraries has become a powerful tool for the evolution of novel ligands that bind virtually any protein target. However, the rules governing conformational preferences in natural peptides are poorly understood, and consequently, structure-activity relationships in these molecules can be difficult to define. In an effort to simplify this process, we have investigated the structural stability of 10-residue, disulfide-constrained beta-hairpins and assessed their suitability as scaffolds for beta-turn display. Using disulfide formation as a probe, relative free energies of folding were measured for 19 peptides that differ at a one strand position. A tryptophan substitution promotes folding to a remarkable degree. NMR analysis confirms that the measured energies correlate well with the degree of beta-hairpin structure in the disulfide-cyclized peptides. Reexamination of a subset of the strand substitutions in peptides with different turn sequences reveals linear free energy relationships, indicating that turns and strand-strand interactions make independent, additive contributions to hairpin stability. Significantly, the tryptophan strand substitution is highly stabilizing with all turns tested, and peptides that display model turns or the less stable C'-C' ' turn of CD4 on this tryptophan "stem" are highly structured beta-hairpins in water. Thus, we have developed a small, structured beta-turn scaffold, containing only natural L-amino acids, that may be used to display peptide libraries of limited conformational diversity on phage.

Disulfides↗

PubMed2001

Remarkable control of radical cyclization processes of cyclic enyne: total syntheses of (+/-)-methyl gummiferolate, (+/-)-methyl 7beta-hydroxykaurenoate, and (+/-)-methyl 7-oxokaurenoate and formal synthesis of (+/-)-gibberellin a(12) from a common synthetic precursor.

Total syntheses of (+/-)-methyl gummiferolate (13b), (+/-)-methyl 7beta-hydroxykaurenoate (14b), and (+/-)-methyl 7-oxokaurenoate (14d) and a formal synthesis of (+/-)-gibberellin A(12) (15) have been accomplished through the common synthetic precursor, (3aR,7aR)-3,3-dimethyl-7a-(2-propynyl)-3a,4,7,7a-tetrahydroisobenzofuranone (16). The homoallyl-homoallyl radical rearrangement reaction of the monocyclic enyne 25, derived from 16 in two steps, afforded the bicyclo[2.2.2]octane compound 26, which was converted to (+/-)-methyl gummiferolate (13b). In contrast, the radical cyclization of the bicyclic enyne 16 gave the tricyclic lactone 19, leading to (+/-)-methyl 7beta-hydroxykaurenoate (14b) and (+/-)-methyl 7-oxokaurenoate (14d). Transformation of 14d into lactone 20 was carried out in a single step under bromination conditions. This constitutes a formal total synthesis of gibberellin A(12) (15).

Journal Article↗

PubMed2001

Use of aromatic radical-anions in the absence of THF. Tandem formation and cyclization of benzyllithiums derived from the attack of homo- and bishomoallyllithiums on alpha-methylstyrenes: two-pot synthesis of cuparene.

When a homo- or bishomoallyllithium, generated by reductive lithiation of the corresponding phenyl thioether by the radical anion lithium 1-(dimethylamino)naphthalenide (LDMAN), is added to alpha-methylstyrene, a tandem addition/cyclization to a phenyl-substituted five- or six-membered-ring occurs. The yields are compromised by polymerization of the alpha-methylstyrene, a process favored by tetrahydrofuran (THF), the solvent used to generate lithium aromatic radical anions. Thus, a new method of generating LDMAN (unsuccessful for other common radical anions) in the absence of THF has been developed. The radical anion can be generated and the reductive lithiation performed in dimethyl ether at -70 degrees C. After the addition of diethyl ether or other solvent, and evaporation of the dimethyl ether in vacuo, the alpha-methylstyrene is added and the solution is warmed to -30 degrees C. When the unsaturated alkyllithium is primary, no adduct forms in THF due to polymerization of the alpha-methylstyrene, but moderate yields are attained in a solvent containing mainly hexanes. It was also found that the cyclized organolithiums, which would have become protonated in the presence of THF, can be captured by an electrophile, even at ambient temperature. A two-pot synthesis, the most efficient reported, of the sesquiterpene (+/-)-cuparene in 46% yield, using this technology is reported.

Journal Article↗

PubMed2002

Iodine(V) reagents in organic synthesis. Part 1. Synthesis of polycyclic heterocycles via Dess-Martin periodinane-mediated cascade cyclization: generality, scope, and mechanism of the reaction.

The scope, generality, and mechanism of the Dess-Martin periodinane-mediated cyclization reaction of unsaturated anilides discovered during the total synthesis of the CP-molecules (phomoidrides A and B) are delineated. A plethora of heterocyclic compounds are accessible by employing gamma,delta-unsaturated amides (derived from anilines and carboxylic acids), urethanes, or ureas (derived from isocyanates and allylic alcohols and amines) as substrates. Optimization of the reaction led to room-temperature conditions, while isotope labeling studies allowed a mechanistic rationale for this cascade reaction.

Anilides↗

PubMed2002

Iodine(V) reagents in organic synthesis. Part 3. New routes to heterocyclic compounds via o-iodoxybenzoic acid-mediated cyclizations: generality, scope, and mechanism.

The discovery and development of the o-iodoxybenzoic acid (IBX) reaction with certain unsaturated N-aryl amides (anilides) to form heterocycles are described. The application of the method to the synthesis of delta-lactams, cyclic urethanes, hydroxy amines, and amino sugars among other important building blocks and intermediates is detailed. In addition to the generality and scope of this cyclization reaction, this article describes a number of mechanistic investigations suggesting a single electron transfer from the anilide functionality to IBX and implicating a radical-based mechanism for the reaction.

Amines↗

PubMed2002

A solid-phase approach to mouse melanocortin receptor agonists derived from a novel thioether cyclized peptidomimetic scaffold.

The solid-phase synthesis of a novel thioether cyclized peptidomimetic scaffold, displaying functionality at the i to i + 3 positions, is reported. The thioether bridge is formed on-bead by an intramolecular reaction between a chloroacetylated reduced peptide bond and the free thiol from a cysteine. The crude products were obtained in moderate to very high purity. A series of 19 compounds were prepared and tested for agonist activity at the mouse melanocortin receptors 1, 3, 4, and 5 (mMC1-5R). From these results, several compounds were identified as having low micromolar agonist activity at the mMC1R and mMC4R. The former is involved in skin pigmentation and animal coat coloration. The latter is involved in the regulation of appetite and food intake and is currently a drug target for potential treatment of obesity. The most potent compound 1n with the pharmacophore motif "His-DPhe-Arg-Trp" was identified as having an EC(50) value of 165 nM at mMC1R, 7600 nM at mMC3R, 650 nM at mMC4R, and 335 nM at mMC5R. In addition, some of the compounds showed moderate selectivity for the mMC1R.

Amino Acids↗