Bicyclic Analogues Research Articles

An α-d-Configured Bicyclic Nucleoside Restricted in an E-type Conformation: Synthesis and Parallel RNA Recognition

An alpha-D-arabino configured bicyclic nucleoside strongly restricted in an E-type conformation by a 2'-3'-fused oxetane ring is synthesized. Several synthetic strategies toward the target compound are described, and the successful preparation from a D-xylose derivative is based on a ruthenium-mediated cleavage of a double bond, an S(N)2-inversion at the 2-position to give an arabino-configuration, nucleobase coupling, and finally ring closure to give the oxetane ring. The E-type conformation is confirmed by molecular modeling and NMR. The nucleoside is incorporated into short alpha-DNA sequences. In a mixed pyrimidine context, these recognize complementary parallel RNA-sequences with mainly increased affinity and complementary parallel DNA-sequences with decreased affinity. The present bicyclic analogue represents the first conformationally restricted alpha-DNA-analogue to improve nucleic acid recognition in mixmers with alpha-DNA monomers.

Photoinduced Bergman Cycloaromatization of Imidazole‐Fused Enediynes.

AbstractFor Abstract see ChemInform Abstract in Full Text.

αv Integrin Affinity/Specificity and Antiangiogenesis Effect of a Novel Tetraaza Cyclic Peptide Derivative, SU015, in Various Species: [RETRACTED

The present study was undertaken to define the alpha v beta3 and alpha v beta5 binding potency and specificity of SU015, an integrin antagonist. SU015 inhibited alpha v beta3-mediated human umbilical vein endothelial cell or 293/beta3-transfected CHO cell adhesion to fibrinogen, with IC50 values of 0.21 +/- 0.11 muM and 0.32 +/- 0.02 microM. SU015 demonstrated comparable affinity to alpha v beta5 as compared with alpha v beta3 affinity, as well as a relatively high degree of specificity for human alpha v beta3- and alpha v beta5-mediated functions, as compared with other human integrins, including alphaIIbbeta3 (IC50 >100 microM), alpha5/beta1 (IC50 >100 microM), and alpha4/beta1 (IC50 >100 microM). SU015 demonstrated different degrees of species specificity in blocking alpha v beta3-mediated cellular adhesion, with relatively higher affinity to monkey (IC50 = 0.10 microM) and dog (IC50 = 1.30 microM) endothelial or smooth muscle cell alpha v beta3-mediated adhesion. Additionally, SU015 demonstrated a high degree of alpha v beta3 and alpha v beta5 specificity as compared with alpha4beta1-, alpha5beta1-, or alpha IIb beta3-mediated binding in the above species. In conclusion, SU015 is an alpha v beta3 and alpha v beta5 antagonist with relatively higher potency and specificity as compared with alpha IIb beta3, alpha5beta1, or alpha4beta1 integrins. Additionally, comparable alpha v beta3 and alpha v beta5 affinity for SU015 was demonstrated with human and monkey endothelial cells. These data also suggest that this bicyclic RGD analogue linked to a linker at the bottom leaves the RGD at the top available for binding and allows for conjugation with radioisotope for imaging and radiotherapy.

Fluorescent 7‐Deazapurine Derivatives from 5‐Iodocytosine via a Tandem Cross‐Coupling—Annulation Reaction with Terminal Alkynes.

AbstractFor Abstract see ChemInform Abstract in Full Text.

Solid-phase synthesis of α-substituted proline hydantoins and analogs

The manual solid-phase preparation of racemic α-substituted bicyclic proline hydantoins and analogs, which can potentially contain up to four sites of structural diversity (ring size and substitution on the ring or at the ring fusion), is described. Key steps involved alkylation of aldimines of resin-bound amino acids with α,ω-dihaloalkanes and intramolecular displacement of the halide to generate α-substituted prolines and homologs. After formation of resin-bound ureas by reaction of these sterically-hindered secondary amines with isocyanates, base-catalyzed cyclization/cleavage yielded the desired hydantoin products.

Bicyclic nucleoside analogues from d-glucose: synthesis of chiral as well as racemic 1,4-dioxepane ring-fused derivatives

The dioxepanofuranose derivatives 4 and 12, obtained through the cyclization of the 3-(2-hydroxyethyl) ether of a d- xylo-pentodialdose derivative, were appropriately functionalized and elaborated to the first examples of the new class of 3′- O and 5′- O-bicyclic nucleoside analogues 9, 10, and 14 with a fused seven-membered ring. Reactions carried out through the intermediacy of the d- xylo-pentodialdose derivative 5 yielded racemic products, while prior protection of the 4-formyl group (as in 7) before deprotection of the 1,2-hydroxyl groups led to optically active analogues.

Photoinduced Bergman cycloaromatization of imidazole-fused enediynes

A series of 4,5-bis-(alkyn-1-yl)imidazoles—‘imidazole-fused’ enediynes—were synthesized and their reactivities in photoinduced Bergman cycloaromatization reactions were determined. The more conformationally rigid analogues gave cycloaromatized products in good yields upon irradiation (450 W low-pressure mercury lamp, ambient temperature). A bicyclic analogue ( 3 ) was shown to cleave supercoiled plasmid DNA.

Ocular pharmacology of bicyclic hexahydroaporphines

This paper explores the ocular hypotensive actions of bicyclic analogs of hexahydroaporphine (HHA), specifically nor-HHA, in an attempt to shed light on the mechanism(s) by which they lower intraocular pressure (IOP). Studies involving the measurement of IOP and aqueous humor production were conducted in ocular normotensive albino rabbits, while those involving smooth muscle contractility utilized isolated bovine iris. The ability of nor-HHA to produce a sustained drop in IOP is linked to both a functioning adrenergic nervous system and the availability of the products of cyclooxygenase metabolism. Although aqueous flow is not impacted by the bicyclic structures, the significant enhancement of outflow facility points to a probable mechanism of IOP-lowering action. Nor-HHA had no direct contractile or relaxant action on bovine irides, but does cause a concentration-dependent inhibition of carbachol-evoked contractions. This inhibition was reversed by inhibitors of phospholipase A(2) and cyclooxygenase, but not by inhibitors of lipoxygenase, again indicating a role for prostaglandins in the ocular pharmacological action of bicyclic HHAs. Pretreatment with a nitric oxide (NO) scavenger also reversed the ability of nor-HHA to inhibit carbachol-induced contractions, implying a role for NO in the postjunctional actions of HHAs.

Bicyclic Nucleoside Inhibitors of Varicella-Zoster Virus Modified on the Sugar Moiety: 3′ and 5′ Derivatives

Bicyclic furanopyrimidine nucleoside analogues (BCNAs) have been previously reported as potent and selective anti-varicella-zoster virus (VZV) agents. Few modifications on the sugar moiety have been considered so far but some of them have shown interesting activity against human cytomegalovirus (HCMV) while losing activity against VZV. In addition, recent work has led to an entirely new series of anti-HCMV bicyclic furopyrimidine agents, acting through a non-nucleoside mechanism. In order to further investigate structure-activity relationship studies on the sugar moiety, some 3'- and 5'-chloro derivatives and 5'-deoxygenated derivatives have been synthesized. The lack of anti-VZV activity of the 5'-modified derivatives is further proof of a mechanism of action involving VZV thymidine kinase (TK)-mediated phosphorylation. Similarly, the replacement of the 3'-OH with chlorine showed a decrease of antiviral activity, which can be correlated to the lack of interaction with VZV TK as demonstrated by enzyme assays. These results confirm free 5'-OH and 3'-OH as necessary requirements for efficient recognition by VZV TK and for potent anti-VZV activity in cell culture.

Coupled Hydrogen‐Bonding Networks in Polyhydroxylated Peptides

Information transfer: Crystal structures of bicyclic dipeptide analogues within oligopeptides are described for the first time. The bicyclic dipeptides occupy the i to i+1 positions of either βI or βII turns. The rigidified dipeptides form hydrogen-bonding networks which transfer structural information along chains of ambident proton donors and acceptors over several Å (see structures; arrows: hydrogen bonds, red O, blue N, yellow S).

Solvent‐Dependent Conformational Behaviour of Model Tetrapeptides Containing a Bicyclic Proline Mimetic

AbstractTwo model tetrapeptides containing bicyclic analogues of either D‐ or L‐proline were synthesised and their conformational properties were studied by NMR in different solvent systems and by molecular modelling techniques. Compound 1, with the bicyclic D‐proline mimetic in the i+1 position, generated a unique trans isomer, and the peptide showed a well organised structure, in accordance with the tendency of D‐proline to act as a good turn inducer with respect to its enantiomer. Peptide 2 displayed structures equilibrating from type I,II to type VI β‐turns, thus confirming the hypothesised relationship between the chirality of BGS/Bgs and proline enantiomers on nucleating compact turns. Moreover, such behaviour suggested a tool for peptidomimetic design of reverse turn peptides containing BGS/Bgs bicyclic proline mimetics, as the choice of chirality might influence the generation either of compact γ‐ and β‐turns or of flexible equilibrating reverse turn structures. The effect of solvent on conformational behaviour was also studied. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004)

Structural Characterization and Pharmacology of a Potent (Cys101−Cys119, Cys110−Cys117) Bicyclic Agouti-Related Protein (AGRP) Melanocortin Receptor Antagonist

Agouti-related protein (AGRP) is one of two known naturally occurring antagonists of G-protein coupled receptors. AGRP is synthesized in the brain and is an antagonist of the melanocortin-3 and -4 receptors (MC3R, MC4R). These three proteins are involved in the regulation of energy homeostasis and obesity in both mice and humans. The human AGRP protein is 132 amino acids and contains five disulfide bridges in the C-terminal domain. Previous reports of the NMR structures of hAGRP(87-132) and a truncated 34 amino acid form consisting of four disulfide bridges identified that AGRP contains an inhibitor cystine knot (ICK) structural fold, and that is the first mammalian example. Herein, we report a bicyclic hAGRP analogue that, when compared to hAGRP(87-132), possesses equal binding affinity but is 80-fold less potent at the mouse MC4R. Using NMR, computer assisted molecular modeling (CAMM), and cluster analysis, we have identified five structural families, two of which are highly populated, of this bicyclic hAGRP analogue. Computational docking experiments of this bicyclic hAGRP derivative, using a three-dimensional homology molecular model of the mouse MC4R, identified that three of the five structural families could be docked into the MC4R without problems from steric hindrance. Those three docked mMC4R-bicyclic hAGRP family structures were compared with putative hAGRP(87-132) ligand-receptor interactions previously reported (Wilczynski et al. J. Med. Chem. 2004, 47, 2194) in attempts to identify a "bioactive" conformation of the bicyclic hAGRP peptide and account for the 80-fold decreased ligand potency compared to hAGRP(87-132).

In situ 1,3‐Dipolar Azide Cycloaddition Reaction: Synthesis of Functionalized D‐Glucose Based Chiral Piperidine and Oxazepine Analogues.

Abstract Functionalized furanose-fused piperidines 4-6 and oxazepines 15-17 , useful precursors for structurally unique bioactive nucleosides as well as for potential glycosidase inhibitors, have been synthesized by the application of 1,3-dipolar azide cycloaddition (DAC) reaction on d -glucose based substrates. The strategy works well even with the nucleoside analogue 8 , affording the bicyclic nucleoside analogues 11 and 12 .

In situ 1,3-dipolar azide cycloaddition reaction: synthesis of functionalized -glucose based chiral piperidine and oxazepine analogues

Functionalized furanose-fused piperidines 4-6 and oxazepines 15-17, useful precursors for structurally unique bioactive nucleosides as well as for potential glycosidase inhibitors, have been synthesized by the application of 1,3-dipolar azide cycloaddition (DAC) reaction on d-glucose based substrates. The strategy works well even with the nucleoside analogue 8, affording the bicyclic nucleoside analogues 11 and 12.

In situ 1,3-dipolar azide cycloaddition reaction: synthesis of functionalized d-glucose based chiral piperidine and oxazepine analogues

Functionalized furanose-fused piperidines 4- 6 and oxazepines 15- 17 , useful precursors for structurally unique bioactive nucleosides as well as for potential glycosidase inhibitors, have been synthesized by the application of 1,3-dipolar azide cycloaddition (DAC) reaction on d-glucose based substrates. The strategy works well even with the nucleoside analogue 8 , affording the bicyclic nucleoside analogues 11 and 12 .

Photoreactive Bicyclic Amino Acids as Substrates for Mutant Escherichia coli Phenylalanyl-tRNA Synthetases

Unnatural amino acids carrying reactive groups that can be selectively activated under non-invasive biologically benign conditions are of interest in protein engineering as biological tools for the analysis of protein-protein and protein-nucleic acids interactions. The double ring system phenylalanine analogues benzofuranylalanine and benzotriazolylalanine were synthesized, and their photolability was tested by UV irradiation at 254, 320, and 365 nm. Although both showed photo reactivity, benzofuranylalanine appeared as the most promising compound because this amino acid was activated by UVA (long wavelength) irradiation. These amino acids were also tested for in vitro charging of tRNA(Phe) and for protein mutagenesis via the phenylalanyl-tRNA synthetase variant alphaA294G that is able to facilitate in vivo protein synthesis using a range of para-substituted phenylalanine analogues. The results demonstrate that benzofuranylalanine, but not benzotriazolylalanine, is a substrate for phenylalanine tRNA synthetase alphaA294G, and matrix-assisted laser desorption ionization time-of-flight analysis showed it to be incorporated into a model protein with high efficiency. The in vivo incorporation into a target protein of a bicyclic phenylalanine analogue, as described here, demonstrates the applicability of phenylalanine tRNA synthetase variants in expanding the scope of protein engineering.

NMR studies of fully modified locked nucleic acid (LNA) hybrids: solution structure of an LNA:RNA hybrid and characterization of an LNA:DNA hybrid.

LNA is a bicyclic nucleic acid analogue that contains one or more 2'-O,4'-C methylene linkage(s), which effectively locks the furanose ring in a C3'-endo conformation. We report here the NMR solution structure of a nonamer LNA:RNA hybrid and a structural characterization of a nonamer LNA:DNA hybrid, where the LNA strands are composed entirely of LNA nucleotides. This is the first structural characterization of fully modified LNA oligonucleotides. The high-resolution structure reveals that the LNA:RNA hybrid adopts an almost canonical A-type duplex morphology. The helix axis is almost straight and the duplex geometry is regular. This shows that fully modified LNA oligomers can hybridize with complementary RNA and form duplexes within the Watson-Crick framework. The LNA:DNA hybrid structurally resembles an RNA:DNA hybrid as shown by determination of deoxyribose sugar puckers and analysis of NOESY NMR spectra.

Direct isolation of poly(A)+ RNA from 4 M guanidine thiocyanate-lysed cell extracts using locked nucleic acid-oligo(T) capture.

LNA oligonucleotides constitute a class of bicyclic RNA analogues having an exceptionally high affinity for their complementary DNA and RNA target molecules. We here report a novel method for highly efficient isolation of intact poly(A)+ RNA using an LNA-substituted oligo(dT) affinity ligand, based on the increased affinity of LNA-T for complementary poly(A) tracts. Poly(A)+ RNA was isolated directly from 4 M guanidine thiocyanate-lysed Caenorhabditis elegans worm extracts as well as from lysed human K562 and vincristine-resistant K562/VCR leukemia cells using LNA_2.T oligonucleotide as an affinity probe, in which every second thymidine was substituted by LNA thymidine. In accordance with the significantly increased stability of the LNA_2.T-A duplexes in 4 M GuSCN, we obtained a 30- to 50-fold mRNA yield increase using the LNA-substituted oligo(T) affinity probe compared with DNA-oligo(dT)-selected mRNA samples. The LNA_2.T affinity probe was, furthermore, highly efficient in isolation of poly(A)+ RNA in a low salt concentration range of 50-100 mM NaCl in poly(A) binding buffer, as validated by selecting the mRNA pools from total RNA samples extracted from different Saccharomyces cerevisiae strains, followed by northern blot analysis. Finally, we demonstrated the utility of the LNA-oligo(T)-selected mRNA in quantitative real-time PCR by analysing the relative expression levels of the human mdr1 multidrug resistance gene in the two K562 cell lines employing pre-validated Taqman assays. Successful use of the NH2-modified LNA_2.T probe in isolation of human mRNA implies that the LNA-oligo(T) method could be automated for streamlined, high throughput expression profiling by real-time PCR by covalently coupling the LNA affinity probe to solid, pre-activated surfaces, such as microtiter plate wells or magnetic particles.

Studies of Novel Heterocyclic Insensitive High Explosive Compounds: Pyridines, Pyrimidines, Pyrazines and Their Bicyclic Analogues

AbstractThe rationale behind using heterocyclic compounds [1], particularly nitrogen heterocycles, as higher energy insensitive high explosives is discussed, including the potential advantages compared with carbocyclic compounds. The types of functional groups used to impart energy to heterocyclic nuclei, whilst maintaining insensitivity, and methodologies for their introduction, are covered. The latter include nitration (by conventional and clean synthetic methods), amination, and oxidation (on ring heteroatoms and of exocyclic amino groups). Strategies for maximising the energetic content of a given heterocyclic nucleus are also examined. The syntheses of specific examples at QinetiQ are described, based on the following nuclei: pyridine, pyrimidine, pyrazine, quinoxaline, quinazoline, pteridine and purine. Strategies for obtaining the desired amino‐nitro derivatives and their heterocyclic N‐oxides are outlined. Optimisation of the synthetic routes for several candidates is discussed. The physical, explosive and thermal properties of the more successful candidates are described, with suggestions for their potential application in military stores.

Aspartate and glutamate mimetic structures in biologically active compounds.

Glutamate and aspartate are frequently recognized as key structural elements for the biological activity of natural peptides and synthetic compounds. The acidic side-chain functionality of both the amino acids provides the basis for the ionic interaction and subsequent molecular recognition by specific receptor sites that results in the regulation of physiological or pathophysiological processes in the organism. In the development of new biologically active compounds that possess the ability to modulate these processes, compounds offering the same type of interactions are being designed. Thus, using a peptidomimetic design approach, glutamate and aspartate mimetics are incorporated into the structure of final biologically active compounds. This review covers different bioisosteric replacements of carboxylic acid alone, as well as mimetics of the whole amino acid structure. Amino acid analogs presented include those with different distances between anionic moieties, and analogs with additional functional groups that result in conformational restriction or alternative interaction sites. The article also provides an overview of different cyclic structures, including various cycloalkane, bicyclic and heterocyclic analogs, that lead to conformational restriction. Higher di- and tripeptide mimetics in which carboxylic acid functionality is incorporated into larger molecules are also reviewed. In addition to the mimetic structures presented, emphasis in this article is placed on their steric and electronic properties. These mimetics constitute a useful pool of fragments in the design of new biologically active compounds, particularly in the field of RGD mimetics and excitatory amino acid agonists and antagonists.