Three optimized and validated (using accuracy profiles) LC methods for the determination of pentamidine and new analogs in rat plasma

Three novel LC-UV methods for the determination of pentamidine (PTMD) and two of its new analogs in rat plasma are described. The chromatographic conditions (wavelength, acetonitrile percentage in the mobile phase, internal standard) were optimized to have an efficient selectivity. A pre-step of extraction was simultaneously developed for each compound. For PTMD, a solid phase extraction (SPE) with Oasis^® HLB cartridges was selected, while for the analogs we used protein precipitation with acetonitrile. SPE for PTMD gave excellent results in terms of extraction yield (99.7 ± 2.8) whereas the recoveries for the analogs were not so high but were reproducible as well (64.6 ± 2.6 and 36.8 ± 1.6 for analog 1 and 2, respectively).By means of a recent strategy based on accuracy profiles (β-expectation tolerance interval), the methods were successfully validated. β was fixed at 95% and the acceptability limits at ±15% as recommended by the FDA. The method was successfully validated for PTMD (29.6-586.54 ng/mL), analog 1 (74.23-742.3 ng/mL) and analog 2 (178.12-890.6 ng/mL). The first concentration level tested was considered as the LLOQ (lower limit of quantification) for PTMD and analog 1 whereas for analog 2, the LLOQ was not the first level tested and was raised to 178.12 ng/mL.     

Polyimidines,a new class of polymers. II. Polyhexamethylenetetraphenyldithiopyromellitimidine

Polyimidines have been shown to be soluble, thermally stable polymers. In searching for an alternate synthetic method the thio analog of this system has been discovered. The brightly colored (red-orange) perthio derivatives of 3,3-diphenylphthalide and 3,3,5,5-tetraphenyipyromellitide were synthesized from their oxo analogs with P₂S₅. The model compound thioimidines were synthesized by reacting 3,3-diphenyldithiophthalide with aniline and with 1,6-hexane diamine and by reacting 3,3,5,5-tetraphenyltetrathiopyromellitide with aniline and n-hexylamine. The polymerization of tetraphenyltetrathiopyromellitide occurred readily with 1,6-hexanediamine in boiling carbon tetrachloride with complete cyclization. This reaction gave an 80% yield with inherent viscosities up to 0.89 and molecular weights up to approximately 11,000. Thermogravimetric analysis showed a 2% weight loss at 200°C and 10% weight loss at 300°C with rapid decomposition above 300°C. Although the polythioimidine was less thermally stable than its oxo analog, it was much more soluble in common solvents (aromatic and chlorinated aliphatic hydrocarbons) and more readily synthesized in higher yield.     

新型烟酰胺腺嘌呤二核苷酸(NAD)类似物的合成及其辅酶活性

尝试4种形成焦磷酸键的方法合成了5种结构新颖的新型烟酰胺腺嘌呤二核苷酸(NAD)类似物.初步考察了类似物的生物活性,发现苹果酸酶和醇脱氢酶以类似物3b和3d为辅酶时,活性只有以NAD为辅酶时的13%～30%;而以类似物3a,3c和3e为辅酶时,这些酶的活性均极低.     

Characterization of novel nucleoside analogs by electrospray ionization mass spectra

In this paper, we synthesized a novel nucleoside analog by coupling thymine with dimethyl dicarboxylate biphenyl (DDB). The structure of the target compound was determined using 1H nuclear magnetic resonance (NMR) and electrospray ionization tandem mass spectrometry (ESI-MS/MS). The fragmentation pathways were studied in details through ESI-MS/MS. By comparing with unsubstituted nucleosides, such as AZT, MCI, d4T and DDI, it was found that the nucleoside analog coupled with DDB would not yield the daughter ions corresponding to the fragments of the nucleoside base and arabinofuranose analogs, but would lose a neutral molecule HF and DDB easily. However, the unsubstituted nucleosides could lightly yield the fragment ions of the nucleoside base and sugar ring. Hence, electrospray ionization mass spectrometry combined with tandem mass spectrometry (MS/MS) provides a convenient method to recognize the substituted and unsubstituted nucleosides.     

Total synthesis of a novel macrotetrolide

The total synthesis of a novel macrotetrolide, an isobutyl nonactin analog, has been achieved in 15% yield by coupling both enantiomers of the corresponding nonactic acid analogs followed by macrolactonization. These building blocks were prepared starting from β-ketoester in nine steps and 34% overall yield, in an efficient and highly stereoselective sequence. The key steps of the strategy are asymmetric hydrogenation, chelation-controlled allylation, intramolecular haloetherification of bishomoallylic ether presenting a trisubstituted double bond deactivated by an ester, and finally a stereoselective reduction of α-bromoester.     

Synthesis of Phenylalanine Analogs

A straightforward synthesis of phenylalanine analogs is described. Cerium ammonium nitrate (CAN) mediated addition of azide to cinnamic ester, followed by reaction with sodium acetate afforded the α‐azidocinnamate in moderate yield. Hydrogenation of α‐azidocinnamate, followed by BOC, CBZ or Fmoc protection gave phenylalanine analogs. A new approach for synthesizing racemic p‐boronophenylalanine analog was also explored.     

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.     

Heterocyclic compounds. X. A new synthesis of thiadiazasteroids

The reaction of ν-ketoacids or ν-aldehydo acids with o-amino amides results in the formation of 4-quinazolones. Using this reaction a number of polyheterosteroid analogs were synthesized. Thus, when 2-amino-3-carboxamido-4,5,6,7-tetrahydrobenzothiophene (9) was refluxed with levulinic acid (10) in a high boiling solvent, thiadiazasteroid analog (11) was obtained in 78% yield. It was found that this facile one-step reaction could be used to synthesize a variety of tetra and pentacyclic compounds. Nmr spectroscopy was used to assign stereochemistry to the 17-methyl “steroids” (31) and (32).     

Mechanistic study on the facilitation of enzymatic hydrolysis by α-glucosidase in the presence of betaine-type metabolite analogs

Recently we reported that betaine-type metabolite analogs structure-dependently facilitate enzymatic hydrolysis reaction for α-glucosidases, β-glucosidases, and alkaliphosphatases. To understand the facilitation mechanism for enzymes, in this study we expanded the analog library and measured the properties of analog solutions. The structural investigation on α-glucosidase-mediated hydrolysis reaction indicated that suitable structures to facilitate the enzyme reaction efficiently should have the ammonium cation in the betaine structure possess triplicate aliphatic chains from C1 to C7 without any polar functional groups. Analyses of the solution properties revealed that such analogs possess a large hydration layer with low water density. Such a specific hydration environment is generated by the characteristic structure of the betaine-type metabolite analogs. The characteristic hydration indirectly regulates enzyme activity and stability. These findings not only increase our understanding enzyme activation by betaine-type metabolite analogs, but also will contribute to the molecular design of enzyme regulators.     

Enzymatic cyclization reactions of geraniol, farnesol and geranylgeraniol, and those of truncated squalene analogs having C20 and C25 by recombinant squalene cyclase

The substrate specificity of squalene-hopene cyclase was investigated using the C10-C25 analogs including naturally occurring substances, e.g. geraniol (C10), farnesol (C15) and geranylgeraniol (C20). No cyclization occurred for geraniol, but a significantly high conversion ratio (64%) was observed for farnesol, yielding the cyclic sesquiterpenes consisting of 6/6-fused bicyclic ring systems. Among them, an attractive compound having C30 was produced, in the structure of which acyclic the farnesol unit is linked to the bicyclic skeleton through ether linkage. Conversion of geranylgeraniol was low (ca. 12%). The squalene analogs having C20 and C25 also were cyclized in yields of ca. 33-36%, but the analogs having the methyl group at C7 and/or at C11 underwent no cyclization; the large steric bulk size of C7-Me and/or C11-Me, which is arranged in [small alpha]-disposition for all the pre-chair conformation, would have interacted repulsively with the cyclase recognition site near to the C7 and/or C11, resulting in no construction of the all-chair conformation inside the reaction cavity. A relatively low yield of geranylgeraniol indicated that a less bulky hydrogen atom must be located at C14 for the efficient polycyclization reaction. The squalene cyclase shows remarkably broad substrate specificity to accept the truncated analogs having carbon-chain lengths of C(15)-C25 in addition to C30.     

Ring Strain VS. Solvent Effects in Phosphate Base Hydrolysis

To determine the factors governing the enhanced reactivity of 5-membered ring phosphates, the lowest activation free-energy profiles for the alkaline hydrolyses of methyl ethylene phosphate (5-MEP), its acyclic analog, trimethyl phosphate (a-TMP), and its 6-membered ring analog, methyl propylene phosphate (6-MPP), have been computed using ab initio and continuum dielectric methods. The calculations yield product distributions and activation free energy differences in accord with experiment. They show that solvent stabilization of the 5-membered ring transition state plays a key role in the million-fold enhanced rates of alkaline hydrolysis of 5-MEP relative to its acyclic or 6-membered ring analogs. Furthermore, strain energy calculations show that ring strain contributes partly to the observed rate enhancement of 5-MEP relative to 6-MPP but not to that of 5-MEP relative to a-TMP.     

Probing for the Threshold Energy for Visual Transduction: Red-Shifted Visual Pigment Analogs from 3-Methoxy-3-Dehydroretinal and Related Compounds

While azulenic retinal analogs failed to yield a red-shifted visual pigment analog, the 9-cis isomers of the push-pull polyenals 3-methoxy-3-dehydroretinal and 14F-3-methoxy-3-dehydroretinal yielded iodopsin pigment analogs with absorption maxima at, respectively, 663 and 720 nm. The former gave a relatively stable batho product (700 nm) and was able to activate transducin. A lower activity was observed for the latter. One possible explanation for the combined results is that the excitation energies of these red-shifted pigments are approaching the threshold energy for visual transduction (although at this time we cannot rigorously exclude a role of the added F-atom in reducing the transducin activity).     

Thermolysis of Neopentylcobalamin Analogs Complexed to Haptocorrin: Side Chain Entropy and Activation of Organocobalamins for Carbon-Cobalt Bond Homolysis

The kinetics of the thermal Co-C bond homolysis of the complexes of a vitamin B(12) binding protein (haptocorrin) with a series of analogs of neopentylcobalamin modified in side chain structure have been studied. The analogs include the C13 epimer in which the e propionamide side chain adopts an "upwardly" axial conformation and a series of c side chain-modified analogs, including the c-monocarboxylate, the c-N-methylamide, the c-N,N-dimethylamide, and the c-N-isopropylamide. Activation parameters for the thermal homolysis of these complexes show that the previously observed stabilization of alkylcobalamins by haptocorrin is due to both enthalpic and entropic factors. With the exception of that for the analog having the bulkiest c side chain substituent, neopentylcobalamin-c-N-isopropylamide, the enthalpies of activation are independent of analog structure, but the entropies of activation increase with the steric bulk of the c side chain and with the number of "upwardly" projecting side chains, as previously observed for protein-free neopentylcobalamin and its analogs. The results are discussed in terms of the solvent cage effect on Co-C bond homolysis and the importance of corrin ring side chain thermal motions to the entropy of activation for this reaction.     

Synthesis and Antioxidative Properties of 1,2,3,4-Tetrahydropyridine Derivatives with Different Substituents in 4-Position

Natural products are an excellent source of inspiration for the development of new drugs. Among them, betalains have been extensively studied for their antioxidant properties and potential application as natural food dyes. Herein, we describe the seven-step synthesis of new betalamic acid analogs without carboxy groups in the 2- and 6-position with an overall yield of ~70%. The Folin–Ciocalteu assay was used to determine the antioxidant properties of protected intermediate 21. Additionally, the five-step synthesis of betalamic acid analog 35 with three ester moieties was performed. Using NMR techniques, the stability of the obtained compounds towards oxygen was analyzed.     

Enzymatic macrolactonization in the presence of DNA leading to triostin A analogs

Excised thioesterase domains are versatile catalysts for macrocyclization. However, thioesterase-catalyzed cyclization is often precluded due to the occurrence of hydrolysis and product inhibition. To circumvent these obstacles, we devised an unprecedented strategy: coincubation with DNA to capture the cyclic products possessing DNA-binding properties. In experiments involving echinomycin thioesterase-catalyzed macrolactonization leading to the cyclic triostin A analog TANDEM, we found that the addition of DNA drastically improved the yield of TANDEM (19% --> 67%), with a complete reversal of the cyclization:hydrolysis ratio (1:2 --> 18:1). Furthermore, the applicability of this protocol was demonstrated for a variety of substrates. The results described herein provide insight into the mechanism of echinomycin thioesterase-catalyzed conversions and also pave the way for chemoenzymatic synthesis of the quinoxaline antibiotics and their analogs.     

A phosphoramidate substrate analog is a competitive inhibitor of the Tetrahymena group I ribozyme

BACKGROUND: Phosphoramidate oligonucleotide analogs containing N3'-P5' linkages share many structural properties with natural nucleic acids and can be recognized by some RNA-binding proteins. Therefore, if the N-P bond is resistant to nucleolytic cleavage, these analogs may be effective substrate analog inhibitors of certain enzymes that hydrolyze RNA. We have explored the ability of the Tetrahymena group I intron ribozyme to bind and cleave DNA and RNA phosphoramidate analogs. RESULTS: The Tetrahymena group I ribozyme efficiently binds to phosphoramidate oligonucleotides but is unable to cleave the N3'-P5' bond. Although it adopts an A-form helical structure, the deoxyribo-phosphoramidate analog, like DNA, does not dock efficiently into the ribozyme catalytic core. In contrast, the ribo-phosphoramidate analog docks similarly to the native RNA substrate, and behaves as a competitive inhibitor of the group I intron 5' splicing reaction. CONCLUSIONS: Ribo-N3'-P5' phosphoramidate oligonucleotides are useful tools for structural and functional studies of ribozymes as well as protein-RNA interactions.     

Immunological effect of two synthetic peptides containing alanine or D-alanine instead of acetyl group of thymosin beta 4 after treatment of human serum

Two analogs of thymosin beta 4 the N-terminal acetyl groups of which were substituted by Ala or D-Ala, were synthesized by the solution method and studied for their immunological effect on the impaired blastogenic response of T-lymphocytes isolated from uremic patients after treatment of human serum. One of the synthetic analogs, D-Ala-thymosin beta 4 demonstrated a restorative effect on these patients when incubated in human serum, but the other analog, Ala-thymosin beta 4, showed no restorative effect under the same conditions. These results seem to suggest that D-Ala-thymosin beta 4 increases resistance to proteolytic degradation by exopeptidases more than Ala-thymosin beta 4.     

Highly efficient modification of DNA polymerase β under conditions of direct and sensitized activation of photoreactive DNAs. Modification of cell extract proteins

dUTP and dCTP derivatives containing a 4-azido-2,3,5,6-tetrafluorobenzylideneaminooxy group were incorporated into the 3′-end of the DNA primer within complexes with the DNA-matrix as analogs of natural dTTP by virtue of catalytic activity of DNA polymerase β or endogenous DNA polymerases of the cell extract. The photoreactive DNAs synthesized in situ were used for affinity modification of DNA polymerase β and DNA-binding proteins of the cell extract. For the photoreactive DNA based on these analogs, the efficiency of formation of covalent adducts with DNA polymerase β under the highest degree of DNA complexation with the enzyme was determined. The yield of covalent DNA adducts with the enzyme was 28–47%, depending on the type of the analog. The effect of the sequence of the DNA template near the localization of the photoreactive group on the redistribution of covalent cross-links between the possible targets was demonstrated. A possibility of increasing the efficiency of DNA polymerase β modification in the presence of a substantial excess of photoreactive DNA using a sensitizer, a dUTP derivative containing a pyrene residue, was studied. When photoreactive DNA containing a 2,3,5,6-tetrafluoro-4-azidobenzoyl (FAB) group was used, about 60% of DNA polymerase β was covalently attached to DNA. Photoreactive dNTP analogs ensuring a high level of protein modification in the cell extract were found. __________ Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 5, pp. 1273–1283, May, 2005.