NMR solution structure of dsDNA containing a bicyclic D-arabino-configured nucleotide fixed in an O4'-endo sugar conformation

[3.2.0]bcANA is a D-arabino-configured bicyclic nucleotide with a 2'-O,3'-C-methylene bridge. We here present the high-resolution NMR structure of a [3.2.0]bcANA modified dsDNA nonamer with one modified nucleotide incorporated. NOE restraints were obtained by analysis of NOESY cross peak intensities using a full relaxation matrix approach, and subsequently these restraints were incorporated into a simulated annealing scheme for the structure determination. In addition, the furanose ring puckers of the deoxyribose moieties were determined by analysis of COSY cross peaks. The modified duplex adopts a B-like geometry with Watson-Crick base pairing in all base pairs and all glycosidic angles in the anti range. The stacking arrangement of the nucleobases appears to be unperturbed relative to the normal B-like arrangement. The 2'-O,3'-C-methylene bridge of the modified nucleotide is located at the brim of the major groove where it fits well into the B-type duplex framework. The sugar pucker of the [3.2.0]bcANA nucleotide is O4'-endo and this sugar conformation causes a change in the delta backbone angle relative to the C2'-endo deoxyribose sugar pucker. This change is absorbed locally by slight changes in the epsilon and zeta angles of the modified nucleotide. Overall, the [3.2.0]bcANA modifications fits very well into a B-like duplex framework and only small and local perturbations are observed relative to the unmodified dsDNA of identical base sequence.     

Synthesis of a novel bicyclic nucleoside restricted to an S-type conformation and initial evaluation of its hybridization properties when incorporated into oligodeoxynucleotides.

The phosphoramidite (1S,3R,4S)-3-(2-cyanoethoxy(diisopropylamino)phosphinoxymethyl)-5-N-(4-monomethoxytrityl)-1-(uracil-1-yl)-5-aza-2-oxabicyclo[2.2.1]heptane 18 of a novel bicyclic nucleoside structure was synthesized from the known 1-(3'-deoxy-beta-D-psicofuranosyl)uracil 3. Conformational analysis of its structure verified its expected S-type furanose conformation, and the secondary amino group in the 4'-position allowed for incorporation into oligonucleotides using 5' --> 3' directed oligonucleotide synthesis as previously described for phosphoramidates. Thermal denaturation studies showed rather large decreases in duplex stabilities of -4.3 and -2.7 degrees C per modification toward complementary DNA and RNA, respectively.     

An alpha-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.     

Stabilisation of the type I β-turn conformation by a bicyclic analogue of proline

A highly constrained analogue of l-proline, (1S,2S,4R)-2-phenyl-7-azabicyclo[2.2.1]heptane-1-carboxylic acid, has been incorporated into a model dipeptide. X-Ray diffraction analysis has shown that, in the solid state, this constrained peptide adopts a type I β-turn whereas the analogous dipeptide sequence incorporating l-proline has been shown to accommodate a βII-turn disposition. Attractive interactions involving the middle NH group and either the aromatic rings or the pyramidalised bicycle nitrogen seem to play a role in the stabilisation of the βI-turn conformation observed.     

Synthesis of a conformationally restricted substrate analogue of siderophore biosynthetases

[reaction: see text] A conformationally restricted analogue (5) of N(omega)-acetyl-N(omega)-hydroxyornithine and -lysine was synthesized. The synthesis features an efficient acylnitroso hetero-Diels-Alder cycloadduct (1) ring opening with palladium(0) and methylnitroacetate.     

Synthesis of pyrrolidinone PNA: a novel conformationally restricted PNA analogue

To preorganize PNA for duplex formation, a new cyclic pyrrolidinone PNA analogue has been designed. In this analogue the aminoethylglycine backbone and the methylenecarbonyl linker are connected, introducing two chiral centers compared to PNA. The four stereoisomers of the adenine analogue were synthesized, and the hybridization properties of PNA decamers containing one analogue were measured against complementary DNA, RNA, and PNA strands. The (3S,5R) isomer was shown to have the highest affinity toward RNA, and to recognize RNA and PNA better than DNA. The (3S,5R) isomer was used to prepare a fully modified decamer which bound to rU10 with only a small decrease in Tm (delta Tm/mod = 1 degree C) relative to aminoethylglycine PNA.     

Synthesis of a novel 3, 4-dihydromilbemycin analogue.

The synthesis of a 3, 4-dihydromilbemycin derivative has been achieved by Julia coupling of the trianion of a C-1 to C-10 ‘southern’ fragment with a C-11 to C-25 ‘northern’ unit.     

Synthesis of an analogue of lavendamycin and of conformationally restricted derivatives by cyclization via a hemiaminal intermediate

Quinoline 12 was obtained by a Friedländer reaction from 2-aminobenzaldehyde and methyl acetoacetate. Reduction, silylation then oxidation provided compound 8a. A Pictet-Spengler reaction between the latter and tryptophan methyl ester yielded compound 14, then compound 7 by desilylation. Numerous attempts to prepare a cyclized derivative of this analogue of lavendamycin 7 by conventional ways failed. Fortunately, a good result was obtained via a hemiaminal intermediate and compound 21 was thus obtained in satisfactory yield. A conjugate addition occurred in the course of its reduction which led to compound 22. Biological tests were carried out with compound 7 and the conformationally restricted analogues 21 and 22.     

Synthesis of 5-homologous AZT and D4T derivatives.

The 3'-iodonucleosides 4 have been synthesized by condensation of silylated 5-alkyluracils 2 with methyl 5-O-tert-butyldiphenylsilyl-2,3-dideoxy-3-iodo-D-threo-pentofur anoside (3). 4 was treated with sodium azide and the deprotected nucleoside 5 was subsequently obtained by treatment with tetrabutylammonium fluoride. The nucleoside 4 produced the corresponding 2',3'-didehydro-2',3'-dideoxy nucleoside 6 and 3',4'-didehydro-2',3'-dideoxy nucleoside 7 in elimination reactions on treatment with sodium methoxide.     

Synthesis and chemistry of unusual bicyclic endoperoxides containing the pyridazine ring

Inverse-Diels-Alder reaction of dimethyl 1,2,4,5-tetrazine-3,6-dicarboxylate with unsaturated bicyclic endoperoxides gave the bicyclic endoperoxides containing the pyridazine ring. The NEt(3) and CoTPP (TPP = tetraphenylporphyrin) catalyzed reaction of endoperoxide 8 resulted in the formation of hydroxy ketone 11 and cis-diol 9. Cleavage of the peroxide linkage in 8 with thiourea provided cis-diol 9. Oxidation of hydroxy ketone 11 and cis-diol 9 led to the phthalazine-5,8-dione 10. Furthermore, the various transformations of the other endoperoxides 19, 20, 22, 23, and 30 resulted in the formation of pyridazine derivatives.     

Synthesis and properties of a new fluorescent bicyclic 4-N-carbamoyldeoxycytidine derivative

[reaction: see text] A bicyclic 4-N-carbamoyldeoxycytidine derivative (1, dC(hpp)) geometrically locked was synthesized as a new fluorescent nucleobase. The hybridization properties of oligodeoxynucleotides containing dC(hpp) were investigated by use of T(m) analysis. It was found that dC(hpp) forms stable base pairs not only with the complementary guanine base, but also with the adenine base. Interestingly, the fluorescence of dC(hpp) was suppressed only when a dC(hpp)-dG base pair was formed.     

First synthesis of 4'-selenonucleosides showing unusual Southern conformation

The first synthesis of 4'-selenonucleosides was achieved using a Pummerer-type condensation as a key step. All stereoelectronic effects shown in 4'-oxonucleosides were overwhelmed by the size of selenium and steric interactions, driving the conformation to the C2'-endo/ C3'-exo twist (Southern) conformation.     

A cyclopentadienide analogue containing divalent germanium and a heavy cyclobutadiene-like dianion with an unusual Ge4 core

The first isolable cyclogermylidenide salt 2 has been synthesized and isolated by facile dehalogenation of the N-heterocyclic chlorogermylene 1 with elemental potassium in ether and isolated in the form of yellow crystals in 33% yield. Single-crystal X-ray diffraction analysis revealed that 2 crystallizes as a dimeric half-sandwich complex of aromatic C3NGe rings interconnected via intermolecular Ge(II)-->K dative bonds. Its yield can be improved up to 42% by gentle reduction of 1 (or its related GeCl3 complex 8) using potassium graphite. Additionally, the remarkable K2Ge4 cluster compound 9 has been isolated as a side product which consists of an unusual dianionic Ge4 core with parallelogram configuration and pronounced aromaticity as indicated by highly negative NICS values.     

Synthesis of a bicyclic double-headed nucleoside

An attempt of preparing a carbocyclic LNA-analogue using different RCM-methods failed. However, a compound with a hemiacetal linker between the C2′ and the C4′-positions was isolated and found to be a suitable substrate for making a conformationally restricted double-headed nucleoside. This contains two uracil nucleobases organized on a bicyclic skeleton and is locked in an N-type conformation.     

Efficient synthesis of a new pipecolic acid analogue with a bicyclic structure

This report describes the synthesis of 2-azabicyclo[2.2.2]octane-1-carboxylic acid, a constrained pipecolic acid analogue. The route gives a very good total yield starting from cheap and readily available compounds and uses very easy reactions.     

Preparation of an analogue of orbicuside A,an unusual cardiac glycoside

A steroid containing a multi-linked glycoside, analogous to the bufadienolide orbicuside A, has been prepared. The key steps were (i) the preparation of a 2α-allyloxycarbonyloxy-3β-hydroxy steroid, (ii) a Ferrier reaction between the steroid and a rhamnal derivative, (iii) removal of protecting group and oxidation of the 2-hydroxy group, (iv) dihydroxylation of the pseudoglycal from the sterically more hindered side and finally (v) ring closure by acetal formation under acidic conditions.     

Synthesis of oxepane ring containing monocyclic, conformationally restricted bicyclic and spirocyclic nucleosides from D-glucose: a cycloaddition approach

Carbohydrate-derived substrates having (i) C-5 nitrone and C-3-O-allyl, (ii) C-4 vinyl and a C-3-O-tethered nitrone, and (iii) C-5 nitrone and C-4-allyloxymethyl generated tetracyclic isoxazolidinooxepane/-pyran ring systems upon intramolecular nitrone cycloaddition reactions. Deprotection of the 1,2-acetonides of these derivatives followed by introduction of uracil base via Vorbrüggen reaction condition and cleavage of the isooxazolidine rings as well as of benzyl groups by transfer hydrogenolysis yielded an oxepane ring containing bicyclic and spirocyclic nucleosides. The corresponding oxepane based nucleoside analogues were prepared by cleavage of isoxazolidine and furanose rings, coupling of the generated amino functionalities with 5-amino-4,6-dichloropyrimidine, cyclization to purine rings, and finally aminolysis.     

Synthesis and structure of noncondensed bicyclic thiazolidino-4-one derivatives

The synthesis of novel noncondensed bicyclic thiazolidin-4-one derivatives has been achieved. The bond between the thiazolidinone rings has been shown, using mass spectrometry, to be located at the 5–4 positions.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 11, pp. 1568–1571, November, 1987.     

Isosteres of natural phosphates. 11. Synthesis of a phosphonic acid analogue of an oligonucleotide

The synthesis of an isosteric phosphonic acid analogue of UpUpU has been accomplished. In this analogue each of the normal 3'-phosphate esteric oxygen atoms has been replaced with a methylene group. The synthesis began with diacetone-D-glucose which was converted in a series of reactions to a 3'-deoxy-3'-dihydroxyphosphinylmethyluridine derivative, which bore protection as a 3-benzoylpropionate at the 5'-hydroxyl and as an acetate at the 2'-hydroxyl. This critical intermediate (A) was condensed with 2',3'-O-isopropylidene uridine to generate a protected analogue of a dinucleoside phosphate. Selective removal of the 3-benzoylpropionate followed by condensation with another unit of (A) yielded the protected oligonucleotide. Deprotection was accomplished in two steps.