Constraints of opsin structure on the ligand-binding site: studies with ring-fused retinals

Ring-fused retinal analogs were designed to examine the hula-twist mode of the photoisomerization of the 9-cis retinylidene chromophore. Two 9-cis retinal analogs, the C11-C13 five-membered ring-fused and the C12-C14 five-membered ring-fused retinal derivatives, formed the pigments with opsin. The C11-C13 ring-fused analog was isomerized to a relaxed all-trans chromophore (lambda(max) > 400 nm) at even -269 degrees C and the Schiff base was kept protonated at 0 degrees C. The C12-C14 ring-fused analog was converted photochemically to a bathorhodopsin-like chromophore (lambda(max) = 583 nm) at -196 degrees C, which was further converted to the deprotonated Schiff base at 0 degrees C. The model-building study suggested that the analogs do not form pigments in the retinal-binding site of rhodopsin but form pigments with opsin structures, which have larger binding space generated by the movement of transmembrane helices. The molecular dynamics simulation of the isomerization of the analog chromophores provided a twisted C11-C12 double bond for the C12-C14 ring-fused analog and all relaxed double bonds with a highly twisted C10-C11 bond for the C11-C13 ring-fused analog. The structural model of the C11-C13 ring-fused analog chromophore showed a characteristic flip of the cyclohexenyl moiety toward transmembrane segments 3 and 4. The structural models suggested that hula twist is a primary process for the photoisomerization of the analog chromophores.     

Synthesis of 2'-O-[2-[(N,N-dimethylamino)oxy]ethyl] modified nucleosides and oligonucleotides.

A versatile synthetic route has been developed for the synthesis of 2'-O-[2-[(N,N-dimethylamino)oxy]ethyl] (abbreviated as 2'-O-DMAOE) modified purine and pyrimidine nucleosides and their corresponding nucleoside phosphoramidites and solid supports. To synthesize 2'-O-DMAOE purine nucleosides, the key intermediate B (Scheme 1) was obtained from the 2'-O-allyl purine nucleosides (13a and 15) via oxidative cleavage of the carbon-carbon bond to the corresponding aldehydes followed by reduction. To synthesize pyrimidine nucleosides, opening the 2,2'-anhydro-5-methyluridine 5 with the borate ester of ethylene glycol gave the key intermediate B. The 2'-O-(2-hydroxyethyl) nucleosides were converted, in excellent yield, by a regioselective Mitsunobu reaction, to the corresponding 2'-O-[2-[(1,3-dihydro-1,3-dioxo-2H-isoindol-2-yl)oxy]ethyl] nucleosides (18, 19, and 20). These compounds were subsequently deprotected and converted into the 2'-O-[2-[(methyleneamino)oxy]ethyl] derivatives (22, 23, and 24). Reduction and a second reductive amination with formaldehyde yielded the corresponding 2'-O-[2-[(N,N-dimethylamino)oxy]ethyl] nucleosides (25, 26, and 27). These nucleosides were converted to their 3'-O-phosphoramidites and controlled-pore glass solid supports in excellent overall yield. Using these monomers, modified oligonucleotides containing pyrimidine and purine bases were synthesized with phosphodiester, phosphorothioate, and both linkages (phosphorothioate and phosphodiester) present in the same oligonucleotide as a chimera in high yields. The oligonucleotides were characterized by HPLC, capillary gel electrophoresis, and ESMS. The effect of this modification on the affinity of the oligonucleotides for complementary RNA and on nuclease stability was evaluated. The 2'-O-DMAOE modification enhanced the binding affinity of the oligonucleotides for the complementary RNA (and not for DNA). The modified oligonucleotides that possessed the phosphodiester backbone demonstrated excellent resistance to nuclease with t(1/2) > 24 h.     

Interaction between N-phosphoryl-α, β- and γ-amino acids and nucleosides

The reactions of four different N-(O,O′-diisopropyl) phosphoamino acids (DIPP-aa),such as N-phosphoryl-L-α-alanine (DIPP- L-α-Ala),N-phosphoryl-D-α-alanine (DIPP-D-α-Ala),N-phosphoryl-β-alanine (DIPP-β-Ala) and N-phosphoryl-γ-amino butyric acid (DIPP-γ-Aba),and four nucleosides,adenosine (A),guanosine (G),cytidinc (C) and uridine (U),were studied by electrospray ionization tandem mass spectrometry (ESI-MS/MS) and HPLC/ESI-MS.DIPP-L-α-Ala and DIPP-D-α-Ala produced the same phosphorylated nucleosidcs,dinucleotidcs and phosphoroligopeptide.However,DIPP-β-Ala and DIPP-γ-Aba gave no relevant products.     

Comparison of Py*+/dU*- charge transfer state dynamics in 5-(1-pyrenyl)-2'-deoxyuridine nucleoside conjugates with amido-, ethylenyl-, and ethynyl linkers

Femtosecond, picosecond, and nanosecond transient absorbance (TA) and picosecond emission kinetics results are presented for three 5-(1-pyrenyl)-2'-deoxyuridine nucleosides each with a different two-atom linker joining pyrenyl C-1 to uracil C-5. The linkers are respectively -NHCO-, -(CH(2))(2)-, and -C[triple bond]C- for PAdU, PEdU, and PYdU. For all three nucleoside conjugates, most conformers undergo intramolecular charge transfer (CT) from their pyrenyl (1)(pi,pi) excited states to form Py(*+)/dU(*-) CT products in ultrashort times: 相似文献   

Spectroscopic studies and molecular orbital analysis on platinanaphthalenes and ring-fused B-N platinanaphthalenes

The electronic structure and properties of the platinanaphthalenes, and ring-fused B-N platinanaphthalenes isomers have been explored using the hybrid density functional mpw1pw91 theory. The energetic aspect shows that stability of Ptb and Pta isomers are isoenergetic in platinanaphthalenes. On the other hand, BNa1 isomer is the most stable isomer of ring-fused B-N platinanaphthalenes. This is compatible with principles of minimum energy and minimum polarizability in ring-fused B-N platinanaphthalenes. Molecular orbital analysis shows increasing of hardness in ring-fused B-N platinanaphthalenes isomers. Also, electronic spectra analysis indicates that, in all the molecules HOMO-1 → LUMO transition makes the major contribution in most intense electronic transition.     

Azoles as Suzuki cross-coupling leaving groups: syntheses of 6-arylpurine 2'-deoxynucleosides and nucleosides from 6-(imidazol-1-yl)- and 6-(1,2,4-triazol-4-yl)purine derivatives

[reaction: see text] 6-(Imidazol-1-yl)-, 6-(benzimidazol-1-yl)-, and 6-(1,2,4-triazol-4-yl)purine nucleosides undergo a nickel-mediated C-C cross-coupling of azole-substituted purine derivatives with arylboronic acids to give good yields of 6-arylpurine nucleosides.     

Adjacent versus opposite type di-aromatic ring-fused phthalocyanine derivatives: synthesis,spectroscopy, electrochemistry,and molecular orbital calculations

A series of adjacent and opposite type di-aromatic ring-fused phthalocyanines (Pc's) of varying size have been prepared and characterized spectroscopically and electrochemically, and most of their properties have been reasonably reproduced by molecular orbital (MO) calculations. The adjacent isomers alone were obtained preferentially by using a diphthalonitrile unit linked via a short aryl chain. The main results are summarized as follows. (i) The Q-band shifts to longer wavelength and its intensity increases, but the degree of change decreases, with increasing molecular size. On the bases of the experiments and MO calculations, setting the size of the effect of benzene directly fused to the tetraazaporphyrin (TAP) skeleton at unity, the effect of the second and third benzene units is roughly about 0.75-0.80 and 0.48 +/- 0.06, respectively. As a result of this, among compounds having an isomeric pi-system, the Q-band of a D(4h) type species lies at longer wavelength than those of adjacently and oppositely di-aromatic ring-fused species. (ii) The Q-band of adjacently substituted species does not split appreciably, while that of the oppositely substituted species splits substantially, the extent having a parallel relationship with the ratio of long to short axes in the molecule. In general, the larger the ratio, the larger the splitting. (iii) The Q-band of oppositely dibenzo-fused and bis(dialkyl)-substituted TAP does not show explicit splitting because of the large coefficients of the carbons substituted with alkyl groups in the MOs. (iv) Interestingly, the first oxidation in adjacently and oppositely dibenzo-fused CoTAP occurs at the cobalt and ligand, respectively, although they are isomers to each other.     

Pyrrolyl-, 2-(2-thienyl)pyrrolyl- and 2,5-bis(2-thienyl)pyrrolyl-nucleosides: synthesis, molecular and electronic structure, and redox behaviour of C5-thymidine derivatives

A series of modified nucleosides based on thymidine have been prepared by Pd-catalysed cross-coupling between N-alkyl-alkynyl functionalised pyrrolyl- (py), 2-(2-thienyl)pyrrolyl- (tp) or 2,5-bis(2-thienyl)pyrrolyl (tpt) groups with 5-iodo-2'-deoxyuridine. The length of the alkyl chain linking the nucleoside and pyrrolyl-containing unit, N(CH(2))(n)C[triple bond, length as m-dash]C-nucleoside (where n = 1-3) was also varied. The compounds have been characterised by (1)H NMR, ES-MS, UV-vis, cyclic voltammetry (CV) and, in some cases, single-crystal X-ray diffraction. Cyclic voltammetry studies demonstrated that all the py-, tp- and tpt-alkynyl derivatives 1-7 can be electrochemically polymerised to form conductive materials. It was found that increasing the N-alkyl chain length in these cases resulted in only minor changes in the oxidation potential. The same behaviour was observed for the tp- and tpt-modified nucleosides 9-12; however, the py-derivative, 8, produced a poorly conducting material. DFT calculations on the one-electron oxidised cation of the modified nucleosides bearing tp or tpt showed that spin density is located on the pyrrolyl and thienyl units in all cases and that the coplanarity of adjacent rings increases upon oxidation. In contrast, in the corresponding pyrrolyl cases the spin density is distributed over the whole molecule, suggesting that polymerisation does not occur solely at the pyrrolyl-Cα position and the conjugation is interrupted.     

Directed diversity-oriented synthesis. Ring-fused 5- to 10-membered rings from a common peptidomimetic 2-pyridone precursor

A variety of ring-fused 2-pyridone-based central fragments were prepared using a strategy inspired by diversity-oriented synthesis. The produced compounds are diverse, yet focused, analogs of biologically active peptidomimetic 2-pyridones.     

Synthesis and evaluation of dihydroimidazolo and dihydrooxazolo ring-fused 2-pyridones—targeting pilus biogenesis in uropathogenic bacteria

Dihydrothiazolo ring-fused 2-pyridones have previously been shown to inhibit pilus assembly in uropathogenic Escherichia coli. Methods have now been developed to synthesize both dihydroimidazolo and dihydrooxazolo ring-fused 2-pyridones. To obtain the nitrogen analogs, Cbz-protected imidazolines were reacted with an acyl-Meldrum's acid derivative under acidic conditions. To prepare the oxygen analogs, a one-pot procedure was developed that allowed synthesis of dihydrooxazolo ring-fused 2-pyridones starting from acylated serine derivatives. After hydrolysis to their corresponding carboxylic acids and lithium carboxylates, biological evaluation revealed that the sulfur could be replaced by an oxygen atom and still maintains the ability to inhibit pilus assembly in uropathogenic E. coli. However, introducing a secondary amine instead of oxygen resulted in a substantial decrease in biological activity.     

Access to ring-fused homo- and heteroaromatic derivatives via an initial ring-opening of 3-nitro-4-(phenylsulfonyl)thiophene

Within an overall ring-opening/ring-forming protocol, the (E,E)-4-methylthio-2-nitro-3-phenylsulfonyl-1-pyrrolidino-1,3-butadiene (7) [derived from the initial opening of 3-nitro-4-(phenylsulfonyl)thiophene (6) with pyrrolidine and silver nitrate in EtOH] is revealed to be an excellent precursor of nitro(phenylsulfonyl) derivatives of ring-fused aromatic (naphthalene, phenanthrene) or heteroaromatic (benzothiophene) compounds whose substitution pattern cannot be easily achieved by conventional methods. The key step is represented by a thermal electrocyclic rearrangement of (E,E)-1-aryl-4-methylsulfonyl-2-nitro-3-phenylsulfonyl-1,3-butadienes (9), which, thanks to proper geometric and electronic factors, occurs in unprecedentedly mild conditions and is followed by an irreversible, concerted syn beta-elimination of methanesulfinic acid to aromatize the newly formed cyclohexadienic ring.     

Synthesis of aryl ring-fused benzimidazolequinones using 6-exo-trig radical cyclizations

The preparation of alicyclic ring-fused tetracyclic and pentacyclic benzimidazoles containing one and two fused aryl rings, respectively, is achieved conveniently in three steps, including Bu₃SnH-mediated 6-exo-trig cyclization of σ-aryl radicals generated from 1-allyl-2-(ω-bromoaryl)benzimidazoles. Inclusion of 4,7-dimethoxy substituents on the radical precursors allows access to aryl ring-fused benzimidazolequinones, a unique family of potential bioreductive anti-cancer agents.     

Fully Chemical Recyclable Poly(γ-butyrolactone)-based Copolymers with Tunable Structures and Properties

Chinese Journal of Polymer Science - The emerging chemical recyclable polymers, such as poly(γ-butyrolactone) (PGBL) and poly((R)-3,4-trans six-membered ring-fused GBL) (P((R)-M)), provide a...     

Synthesis of heterocyclic ring-fused quinones (microreview)

Chemistry of Heterocyclic Compounds - This microreview presents the data on the methods of synthesis of heterocyclic ring-fused quinones over the period from 2015 to 2021.     

Selective ring contraction of 5-spirocyclopropane isoxazolidines mediated by acids

Thermolysis of 3,4-cis ring-fused 5-spirocyclopropane isoxazolidines 16, 18-21, 33, 34, 38a, and 61, in the presence of a protic acid at 70-110 degrees C, yielded 3,4-cis ring-fused azetidin-2-ones 22-26,41, 42, 46, and 62 with concomitant extrusion of ethylene, in good yields. So far, the collected evidences strongly support a mechanism started by a homolytic cleavage of the protonated N-O bond for the rearrangement of 5-spirocyclopropane isoxazolidines to beta-lactams. Some different competitive pathways can then follow depending on the stability or the stereoelectronic properties of cationic diradical intermediates. The two-step process, intramolecular 1,3-dipolar cycloaddition/thermal rearrangement under acidic conditions, represents a general synthesis of a new class of 3,4-cis-fused bicyclic azetidin-2-ones starting from easily available compounds such as amino acids, hydroxy acids, and dicarbonyl or amino alcohol derivatives.     

Use of 13C as an indirect tag in 15N specifically labeled nucleosides. Syntheses of [8-13C-1,7,NH2-15N3]adenosine, -guanosine, and their deoxy analogues

We have previously reported the use of a 13C tag at the C2 of 15N-multilabeled purine nucleosides to distinguish the adjacent-labeled 15N atoms from those in an untagged nucleoside. We now introduce the use of an indirect tag at the C8 of 15N7-labeled purine nucleosides. This tag allows unambiguous differentiation between a pair of 15N7-labeled purines in which only one is 13C8 labeled. Although the very small C8-N7 coupling (<1 Hz) precludes its direct detection in 1D 15N spectra, 2D 1H-15N NMR experiments display the large C8-H8 coupling (>200 Hz) because H8 is coupled to both N7 and C8. The 13C8 atom is introduced by means of a ring closure of the exocyclic amino groups of a pyrimidinone using [13C]sodium ethyl xanthate. Here, we present methods for the syntheses of [8-13C-1,7,NH2-15N3]adenosine, -guanosine, and their deoxy analogues.     

Exploiting the palladium[0]-catalysed Ullmann cross-coupling reaction in natural products chemistry: application to a total synthesis of the alkaloid (+/-)-aspidospermidine

Azide 14, available through the title cross-coupling process, has been converted, via the ring-fused aziridine 15, into the alkaloid aspidospermidine.     

Unusual deoxygenation and reactivity studies related to O6-(benzotriazol-1-yl)inosine derivatives

New and unusual developments related to the chemistry of O6-(benzotriazol-1-yl)inosine derivatives are reported. First, a simple, scalable method for their syntheses via the use of PPh3/I2/HOBt has been developed and has been mechanistically investigated by 31P(1H) NMR. Studies were then conducted into a unique oxygen transfer reaction between O6-(benzotriazol-1-yl)inosine nucleosides and bis(pinacolato)diboron (pinB-Bpin) leading to the formation of C-6 (benzotriazol-1-yl)purine nucleoside derivatives and pinB-O-Bpin. This reaction has been investigated by 11B(1H) NMR and compared to pinB-O-Bpin obtained by oxidation of pinB-Bpin. The structures of the C-6 (benzotriazol-1-yl)purine nucleosides have been unequivocally established via Pd-mediated C-N bond formation between bromo purine nucleosides and 1H-benzotriazole. Finally, short and extremely simple synthesis of 1,N6-ethano- and 1,N6-propano-2'-deoxyadenosine are reported in order to demonstrate the synthetic versatility of the O6-(benzotriazol-1-yl)inosine nucleoside derivatives for the assembly of relatively complex compounds.     

Extended applications and potential limitations of ring-fused 2,3-oxazolidinone thioglycosides in glycoconjugate synthesis

The utility of ring-fused 2,3-oxazolidinone derivatives of 2-amino-2-deoxy-thioglycosides in the synthesis of glycopeptide intermediates and building blocks for the synthesis of heparan sulfate oligosaccharides is reported. These unique ring-fused monosaccharides afford a novel and efficient route to alpha-O-linked 2-amino-2-deoxy amino acid derivatives and heparan sulfate oligosaccharide intermediates.     

Convenient syntheses of 7-hydroxy-1-(hydroxymethyl)-3-(thymin-1-yl)-2,5-dioxabicyclo

Synthesis of the diastereoisomeric LNA (locked nucleic acid) nucleosides 1-(2-O,4-C-methylene-alpha-L-ribofuranosyl)thymine (6) and 1-(2-O,4-C-methylene-alpha-L-xylofuranosyl)thymine (13) are reported via convenient reaction cascades from di-O-p-toluenesulfonyl and tri-O-methanesulfonyl nucleoside derivatives 3, 7, and 10.