Expanding the genetic alphabet: non-epimerizing nucleoside with the pyDDA hydrogen-bonding pattern

6-Amino-3-(2'-deoxy-beta-D-ribofuranosyl)-5-nitro-1H-pyridin-2-one (4), a C-glycoside exhibiting the nonstandard pyDDA hydrogen-bonding pattern, was synthesized via Heck coupling. The nitro group greatly enhances the stability of the nucleoside toward acid-catalyzed epimerization without leading to significant deprotonation of the heterocycle at physiological pH. These results make nucleoside 4 a promising candidate for an expanded genetic alphabet.     

4-(1-Haloalkyl)-3-nitrotetrahydrofurans as versatile scaffolds for the synthesis of diversely functionalized tetrahydrofurans

4-(1-Haloalkyl)-3-nitrotetrahydrofurans, which are accessible by tandem oxidative oxa-Michael addition/radical cyclization/ligand transfer reactions, can be processed to diversely substituted tetrahydrofuran derivatives. Selective epimerization at the nitro function provides tetrahydrofuran diastereomers, which cannot be prepared by the tandem process. Intramolecular alkylations furnish interesting bridgehead nitro oxabicyclo[3.1.0]hexane derivatives in high yields. Intermolecular substitution reactions of the halide functions succeed only with nucleophiles, which are not basic enough to trigger intramolecular alkylations. The aryl substituent in 2-aryl-3-nitrotetrahydrofurans can be selectively oxidatively transformed to carboxylic acid derivatives using catalytic Ru(III) and NaIO₄ without affecting the nitro group. Reduction and hydrogenation reactions provide differently substituted 3-aminotetrahydrofuran derivatives depending on the conditions with moderate to good chemoselectivity.     

Preparation of α-amino ketones, β-amino hydroxylamines using asymmetric aza-Henry reactions of N-p-tolylsulfinylimines with nitroethane

N-Sulfinylimines derived from aromatic and aliphatic aldehydes react with nitroethane and NaOH, yielding mainly two diastereoisomeric β-nitroamines as the result of a highly diastereoselective reaction and further epimerization of the carbon linked to the nitro group. The resulting β-nitroamines are used as precursors of N-sulfonyl α-amino methyl ketones and β-amino hydroxylamines.     

甲酸铵催化转移氢化还原肽链中的芳香硝基——对氨基苯丙氨酸的间接引入

研究了用甲酸铵催化转移氢化法(AF-CTH)对不同类型肽中的芳香硝基的还原行为, 这些肽类化合物包括促黑激素(MSH: 四肽)、促黄体素释放激素(LHRH: 十肽)和强腓肽(十七肽)的类似物. 用HPLC对还原过程进行了跟踪监测, 结果显示, 除含对氯苯丙氨酸残基的LHRH类似物因发生脱氯副反应不适合用AF-CTH还原外, 其余序列还原过程中均无明显副反应发生, 硝基几乎定量地转化成为相应的氨基, 实现了对氨基苯丙氨酸向肽链的间接引入. 另外发现, 硝基还原所需的时间与肽链长度有关, 肽链越长, 还原所需时间越长, 但与其在序列中的位置关系不明显.     

Charge optimization increases the potency and selectivity of a chorismate mutase inhibitor

The highest affinity inhibitor for chorismate mutases, a conformationally constrained oxabicyclic dicarboxylate transition state analogue, was modified as suggested by computational charge optimization methods. As predicted, replacement of the C10 carboxylate in this molecule with a nitro group yields an even more potent inhibitor of a chorismate mutase from Bacillus subtilis (BsCM), but the magnitude of the improvement (roughly 3-fold, corresponding to a DeltaDeltaG of -0.7 kcal/mol) is substantially lower than the gain of 2-3 kcal/mol binding free energy anticipated for the reduced desolvation penalty upon binding. Experiments with a truncated version of the enzyme show that the flexible C terminus, which was only partially resolved in the crystal structure and hence omitted from the calculations, provides favorable interactions with the C10 group that partially compensate for its desolvation. Although truncation diminishes the affinity of the enzyme for both inhibitors, the nitro derivative binds 1.7 kcal/mol more tightly than the dicarboxylate, in reasonable agreement with the calculations. Significantly, substitution of the C10 carboxylate with a nitro group also enhances the selectivity of inhibition of BsCM relative to a chorismate mutase from Escherichia coli (EcCM), which has a completely different fold and binding pocket, by 10-fold. These results experimentally verify the utility of charge optimization methods for improving interactions between proteins and low-molecular weight ligands.     

Intermediates in the reduction of the antituberculosis drug PA-824, (6S)-2-nitro-6-{[4-(trifluoromethoxy)benzyl]oxy}-6,7-dihydro-5H-imidazo[2,1-b][1,3]oxazine, in aqueous solution

The reduction chemistry of the new anti-tuberculosis drug PA-824, together with a more water-soluble analogue, have been investigated using pulse and steady-state radiolysis in aqueous solution. Stepwise reduction of these nitroimidazo-dihydrooxazine compounds through electron transfer from the CO(2) (-) species revealed that, unlike related nitroimidazoles, 2-electron addition resulted in the reduction of the imidazole ring in preference to the nitro group. In mildly acidic solution a nitrodihydroimidazo intermediate was formed, which was reduced further to the amine product. In both alkaline and neutral solution, an intermediate produced on 2-electron reduction was resistant to further reduction and reverted to parent compound on extraction or mass spectrometric analysis of the solution. The unusual reduction chemistry of these nitroimidazole compounds, exhibiting ring over nitro group reduction, is associated with alkoxy substitution in the 2-position of a 4-nitroimidazole. The unique properties of the intermediates formed on the reduction of PA-824 need to be considered as playing a possible role in its bactericidal action.     

A new and efficient synthesis of pyrrolo[2,3-d]pyrimidine anticancer agents: Alimta (LY231514, MTA), homo-Alimta, TNP-351, and some aryl 5-substituted pyrrolo[2,3-d]pyrimidines

Alimta, as well as homo-Alimta, a nonbridged analogue of Alimta, and TNP-351 have been prepared by a new method that involves Michael addition of the appropriate 1-nitroalkene with 2,6-diamino-3H-pyrimidin-4-one or 2,4,6-triaminopyrimidine, followed by a Nef reaction of the resulting primary nitro Michael adduct. Spontaneous intramolecular cyclization of the resulting aldehyde with the pyrimidine 6-amino group yields the corresponding pyrrolo[2,3-d]pyrimidine. A series of previously unknown 5-arylpyrrolo[2,3-d]pyrimidines was prepared by the same methodology from the above pyrimidines and nitrostyrenes. It has been found that the intermediate primary nitro Michael adduct can be prepared in a single step by sonication of a mixture of an arylaldehyde, nitromethane, and the 6-aminopyrimidine in acetic acid containing ammonium acetate.     

Protophilic isotopic hydrogen exchange of 1-ferrocenyl-2-(nitrophenyl)ethylenes

cis-1-Ferrocenyl-2-(4-nitrophenyl)ethylene enters into the protium/deuterium exchange in basic medium at the expense of hydrogens of the phenyl ring, at ortho positions in respect of the nitro group. The homoaromatic analogue, 4-nitrostilbene, under the same conditions, undergoes isotopic exchange occurring exclusively at the vinylic CH fragment attached to the nitrophenyl group. The difference is eliminated as a result of the shift of the nitro group from position 4 into position 2 of the phenyl ring: cis-1-ferrocenyl-2-(2-nitrophenyl)ethylene enters into H⁺/D⁺ exchange in the same manner as 4-nitrostilbene. Correspondence to: Professor Z.V. Todres.     

Comparative Study of Nitro- and Azide-Functionalized ZnII-Based Coordination Polymers (CPs) as Fluorescent Turn-On Probes for Rapid and Selective Detection of H2S in Living Cells

Selective detection of H₂S in the cellular systems using fluorescent CPs/MOFs is of great scientific interest due to their outstanding aqueous stability, biocompatibility and real-time detection ability. Fabrication of such materials using complete biologically essential elements and applying them as an efficient biosensor is still quite challenging. In this context, two newly synthesized CPs containing biologically essential metal ion (Zn) and nitro/azido functional groups into the framework to sense extracellular and intracellular H₂S by reducing into respective amines are presented. The CP- 1 containing the azide group acted as an efficient fluorescent turn-on probe with the lowest detection limit (7.2 μM) and shortest response time (30 s) among the Zn-based probes reported till date. Moreover, CP- 1 exhibited green luminescence in live cells after imaging a very low concentration of H₂S, whereas the nitro analogue CP- 2 could not detect the target analyte due to its framework disruption.     

Epimerization and racemization of some chiral drugs in the presence of cyclodextrin and liposomes

The effects of alpha-, beta-, gamma- and dimethyl-beta-cyclodextrins (alpha-, beta-, gamma- and DM-beta-CyDs) and liposomes on epimerization or racemization of etoposide, ethiazide and carbenicillin were examined kinetically. alpha- and beta-CyDs accelerated both epimerization and hydrolysis of carbenicillin. They had no effect on epimerization of etoposide, and did not affect racemization and hydrolysis of ethiazide. DM-beta-CyD retarded epimerization of etoposide, hydrolysis of picroetoposide (which is an epimer of etoposide), and racemization and hydrolysis of ethiazide, but had no effect on epimerization and hydrolysis of carbenicillin. gamma-CyD retarded epimerization of etoposide and hydrolysis of picroetoposide. On the other hand, gamma-CyD accelerated epimerization of carbenicillin. It is suggested that the formation of inclusion complexes between CyDs and etoposide, picroetoposide and ethiazide inhibited the attack of bases such as OH- and buffer components, thereby retarding epimerization, racemization and hydrolysis. On the other hand, alpha-, beta- and gamma-CyDs increased the reactivity of carbenicillin through the OH group, accelerating its epimerization and hydrolysis. Liposomes retarded epimerization of etoposide, hydrolysis of picroetoposide and racemization of ethiazide. Liposomes did not affect epimerization and hydrolysis of carbenicillin. These differences in the effect of liposomes on reactivity may be interpreted in terms of the solubility of the drugs.     

Highly conjugated 4-ring nematic liquid crystals with a lateral alkoxy branch

Three types of liquid crystalline compound containing a 4-ring mesogenic core with a lateral alkoxy chain on one of the inner rings were synthesized, and their mesogenic properties studied. The 4-ring core of these compounds bears an electron-accepting nitro group at one end and an electron-donating alkylamino moiety at or near the other end. Therefore, they are highly coloured and have lambda max 473 nm. One of these three types of compound has a wide enantiotropic nematic range. Twelve homologous analogues in this series with different lengths for the terminal alkyl chain and the lateral alkoxy chain were synthesized and compared.     

π-Hole Interactions Involving Nitro Aromatic Ligands in Protein Structures

Studying noncanonical intermolecular interactions between a ligand and a protein constitutes an emerging research field. Identifying synthetically accessible molecular fragments that can engage in intermolecular interactions is a key objective in this area. Here, it is shown that so-called “π-hole interactions” are present between the nitro moiety in nitro aromatic ligands and lone pairs within protein structures (water and protein carbonyls and sulfurs). Ample structural evidence was found in a PDB analysis and computations reveal interaction energies of about −5 kcal mol⁻¹ for ligand–protein π-hole interactions. Several examples are highlighted for which a π-hole interaction is implicated in the superior binding affinity or inhibition of a nitro aromatic ligand versus a similar non-nitro analogue. The discovery that π-hole interactions with nitro aromatics are significant within protein structures parallels the finding that halogen bonds are biologically relevant. This has implications for the interpretation of ligand–protein complexation phenomena, for example, involving the more than 50 approved drugs that contain a nitro aromatic moiety.     

Stereoselective synthesis of azetidine-derived glutamate and aspartate analogues from chiral azetidin-3-ones

The stereoselective syntheses of cis conformationally constrained glutamate and aspartate analogues, containing an azetidine framework were accomplished from (S)-N-tosyl-2-phenylglycine in moderate overall yields. The key steps in these syntheses involved an efficient Wittig olefination of an azetidin-3-one, followed by a highly stereoselective rhodium catalyzed hydrogenation. The route could also be applied to the synthesis of a trans glutamate analogue, since epimerization of cis to trans isomer could be performed using DBU in toluene at reflux.     

Effect of molecular structure on the phase behaviour of some liquid crystalline compounds and their binary mixtures VI[1]. The effect of molecular length

The apparent solution dipole moments of compounds based on 4,4-di-substituted phenyl benzoate (ROC6H4COOC6H4X), I, where X is a cyano group and R a terminal linear alkyl chain ranging from C12 to C20, were determined in cyclohexane at 30 C. The compounds were also thermally characterized by polarized light microscopy and differential scanning calorimetry. Phase diagrams were constructed for various binary mixtures prepared from any two homologues of series I as well as for every one of them with the nitro analogue II, where X is a nitro group and R C16H33. The study was undertaken in order to investigate the effect of the alkyl chain length on the mesophase behaviour. In order to assess the influence of structural variation in the central mesogenic group on the mesophase stability of pure and mixed compounds, the investigation was extended to cover binary mixtures of any two of the three compounds: analogue II (X=OC16H33), and the symmetric dialkoxy substituted phenyl esters (C16H33OC6H4COO)2 A, where A is the 1,4-phenylene group (IV) or 4,4-biphenylene (V).     

Total synthesis and biological evaluation of pacidamycin D and its 3'-hydroxy analogue

Full details of the total synthesis of pacidamycin D (4) and its 3'-hydroxy analogue 32 are described. The chemically labile Z-oxyacyl enamide moiety is the most challenging chemical structure found in uridylpeptide natural products. Key elements of our approach to the synthesis of 4 include the efficient and stereocontrolled construction of the Z-oxyvinyl halides 6 and 7 and their copper-catalyzed cross-coupling with the tetrapeptide carboxamide 5, a thermally unstable compound containing a number of potentially reactive functional groups. This synthetic route also allowed us to easily prepare 3'-hydroxy analogue 32. The assemblage by cross-coupling of the Z-oxyvinyl halide 6 and the carboxamide 5 at a late stage of the synthesis provided ready access to a range of uridylpeptide antibiotics and their analogues, despite their inherent labile nature with potential epimerization, simply by altering the tetrapeptide moiety.     

Basicity of nitropyrazoles and their simultaneous spectrophotometric determination

The protonation constants of some 1-, 3(5)-, 3-, 4- and 5-nitropyrazoles have been determined, and compared with those of nitroimidazoles. The effect of the position of the nitro group in the pyrazole and imidazole ring is discussed. The ortho effects of the nitro group in pyrazole and imidazole are compared and found to have identical values. The effect of the nitro group on protonation constants is greater when the nitro group is close to the pyridine nitrogen atom. This, together with the ability of N-unsubstituted nitropyrazoles to dissociate to give nitropyrazole anions, with an accompanying shift of the spectra to longer wavelengths, permits the simultaneous spectrophotometric determination of nitropyrazoles.     

Differentiation of positional isomers of nitro meso-tetraphenylporphyrins by tandem mass spectrometry

We studied by tandem mass spectrometry two isomers of nitro meso-tetraphenylporphyrin, one with a nitro group in the para position of a phenyl ring and the other with the same group in a beta-pyrrolic position, and their copper complexes. Collisional activation of the molecular ions of both free-base porphyrins and of their copper complexes produces an array of product ions that permit ready differentiation of the two positional isomers. The diagnostic ions, when the nitro group is in a beta-pyrrolic position, may be produced through intramolecular and double cyclization processes, triggered by the interaction of the nitro substituent with the neighboring meso-phenyl ring. These diagnostic ions do not form when the nitro group is in the para position. The gas-phase processes have precedents in solution chemistry.     

Synthesis of 7beta-sulfur analogues of paclitaxel utilizing a novel epimerization of the 7alpha-thiol group

Paclitaxel analogues with a sulfur group at the 7beta position were required for SAR studies. Attempts to generate these compounds by displacing a 7alpha leaving group with sulfur nucleophiles were unsuccessful. Instead, these compounds were successfully prepared from a 7beta-thiol intermediate that was obtained by a base-catalyzed epimerization of the 7alpha-thiol derivative. The epimerization presumably proceeds through a thioaldehyde intermediate and exhibits the opposite stereochemical preference of its oxygen counterpart.     

Reductive transformations of unsaturated azabicyclic nitrolactams

Using different reducing methods unsaturated indolizidine and quinolizidine lactams substituted with a nitro group were transformed into various alkaloid-like derivatives. Hydrogen transfer and palladium catalyzed hydrogenation gave compounds of ketolactam or lactam type meanwhile the nitro group was eliminated. On the other hand, in presence of Raney-nickel catalyst the nitro compounds were reduced to diastereomeric amino derivatives whose stereochemistry was elucidated by NMR spectroscopy. Using sodium bis-dimethoxy-ethoxy-aluminum-hydride (Red-Al) as reducing agent an unexpected tricyclic azetidine was isolated and characterized.     

Aldehyde Intermediates in the Synthesis of Tacamine-Type Indole Alkaloids: Preparation of (±)-apotacamine

The synthesis of aldehyde intermediates suitable for the preparation of indole alkaloids of the tacamine ( 1 ) type is described. The four possible aldehydes 4–7 were prepared from methyl 5-ethylnicotinate ( 8 ) in a few simple steps using a base-catalyzed epimerization as the final step (Schemes 1 and 2). The key aldehyde 4 , which is an analogue of the important vincamine intermediate 3 (‘Oppolzer's aldehyde’), was finally converted into the indole alkaloid (±)-apotacamine ( 21 ).