Combined chromatographic-isotopic dilution analysis of fecapentaenes in human feces

Fecapentaene-12 (FP-12) and fecapentaene-14 (FP-14) are genotoxic unsaturated ether lipids produced by colonic bacteria in man. We have developed and applied to feces collections from normal volunteers direct isotopic dilution procedures using tritium-labeled (at C5) FP-12 and FP-14 for measuring these compounds. FPs were recovered from feces by solvent extraction, silica cartridge clean-up, and analytical liquid chromatography. Low levels of FP-12 and FP-14 (less than 0.1 to 2.4 micrograms/g of freeze-dried feces) were observed. Identity of chromatographic peaks was established by co-elution and by ultraviolet absorption spectra obtained via photodiode array scanning. Two unknown peaks were tentatively identified from absorption spectra as closely related compounds with increased (hexane?) or decreased (tetraene?) number of double bonds. Levels of FPs increased after incubation of feces at 37 degrees C for 96 h under anaerobic conditions and pre-FP-12 and pre-FP-14 peaks were observed, which showed identical spectra with authentic FPs. These were interpreted to be isomeric forms of the all-trans-[3H]FPs used for the isotopic dilution analysis. Total FPs (including pre-FP) yielded a range of 0.3-80 micrograms FP-12 and 2.8-44 micrograms FP-14 per g of freeze-dried feces from the study group.     

In silico identification of noncompetitive inhibitors targeting an uncharacterized allosteric site of falcipain-2

Falcipain-2 (FP-2) is a Plasmodium falciparum hemoglobinase widely targeted in the search for antimalarials. FP-2 can be allosterically modulated by various noncompetitive inhibitors that have been serendipitously identified. Moreover, the crystal structures of two inhibitors bound to an allosteric site, termed site 6, of the homolog enzyme human cathepsin K (hCatK) suggest that the equivalent region in FP-2 might play a similar role. Here, we conduct the rational identification of FP-2 inhibitors through virtual screenings (VS) of compounds into several pocket-like conformations of site 6, sampled during molecular dynamics (MD) simulations of the free enzyme. Two noncompetitive inhibitors, ZINC03225317 and ZINC72290660, were confirmed using in vitro enzymatic assays and their poses into site 6 led to calculated binding free energies matching the experimental ones. Our results provide strong evidence about the allosteric inhibition of FP-2 through binding of small molecules to site 6, thus opening the way toward the discovery of new inhibitors against this enzyme.

     

Recently Developed Concepts for Studying and Understanding the Aggregation of Organic Molecules. Aggregating Tendencies of the Culprits of Arteriosclerosis

Recent developments in research on aggregation and self-coiling of organic molecules are reviewed: structure and medium effects on aggregating tendencies, electrostatically stabilized aggregates (ESAg), co-aggregating tendencies of cholesterols and the effect of chain-folding, and neutral and effective deaggregators (deAgr).     

Identification of novel malarial cysteine protease inhibitors using structure-based virtual screening of a focused cysteine protease inhibitor library

Malaria, in particular that caused by Plasmodium falciparum , is prevalent across the tropics, and its medicinal control is limited by widespread drug resistance. Cysteine proteases of P. falciparum , falcipain-2 (FP-2) and falcipain-3 (FP-3), are major hemoglobinases, validated as potential antimalarial drug targets. Structure-based virtual screening of a focused cysteine protease inhibitor library built with soft rather than hard electrophiles was performed against an X-ray crystal structure of FP-2 using the Glide docking program. An enrichment study was performed to select a suitable scoring function and to retrieve potential candidates against FP-2 from a large chemical database. Biological evaluation of 50 selected compounds identified 21 diverse nonpeptidic inhibitors of FP-2 with a hit rate of 42%. Atomic Fukui indices were used to predict the most electrophilic center and its electrophilicity in the identified hits. Comparison of predicted electrophilicity of electrophiles in identified hits with those in known irreversible inhibitors suggested the soft-nature of electrophiles in the selected target compounds. The present study highlights the importance of focused libraries and enrichment studies in structure-based virtual screening. In addition, few compounds were screened against homologous human cysteine proteases for selectivity analysis. Further evaluation of structure-activity relationships around these nonpeptidic scaffolds could help in the development of selective leads for antimalarial chemotherapy.     

Computer-aided drug design of falcipain inhibitors: virtual screening, structure-activity relationships, hydration site thermodynamics, and reactivity analysis

Falcipains (FPs) are hemoglobinases of Plasmodium falciparum that are validated targets for the development of antimalarial chemotherapy. A combined ligand- and structure-based virtual screening of commercial databases was performed to identify structural analogs of virtual screening hits previously discovered in our laboratory. A total of 28 low micromolar inhibitors of FP-2 and FP-3 were identified and the structure-activity relationship (SAR) in each series was elaborated. The SAR of the compounds was unusually steep in some cases and could not be explained by a traditional analysis of the ligand-protein interactions (van der Waals, electrostatics, and hydrogen bonds). To gain further insights, a statistical thermodynamic analysis of explicit solvent in the ligand binding domains of FP-2 and FP-3 was carried out to understand the roles played by water molecules in binding of these inhibitors. Indeed, the energetics associated with the displacement of water molecules upon ligand binding explained some of the complex trends in the SAR. Furthermore, low potency of a subset of FP-2 inhibitors that could not be understood by the water energetics was explained in the context of poor chemical reactivity of the reactive centers of these compounds. The present study highlights the importance of considering energetic contributors to binding beyond traditional ligand-protein interactions.     

1 - 烃基异喹啉Reissert Compounds 的合成及其氢化研究

1-苄基异喹啉Reissertcompound经RaneyNi(w-2)催化氢化,分离得到二个未见报道的氢化产物,经化学和波谱分析推定其结构为:1-亚氨基-1-苄基-2-苯甲酰基-1,2-二氢异喹啉(4)和3-苯基-10b-苄基-1,10b-二氢咪唑骈[5,1-a]异喹啉(5)。据此提出了一条1-苄基异喹啉Reissertcompound高压催化氢化的途径,并对异喹啉eissertcompound高压催化氢化反应中酰基转位进行了讨论。试图以环已基溴作为烷化剂,在氢化钠条件下,与异喹啉Reissertcompound作用来制备1-环已基异喹啉Reissertcompound,结果只得到了1-氰基异喹啉,产率达75%,为制备1-氰基异喹啉提供了一个新方法。     

Synthesis of the highly potent prostanoid FP receptor agonist, AFP-168: a novel 15-deoxy-15,15-difluoroprostaglandin F2α derivative

A novel 15-deoxy-15,15-difluoro-prostaglandin(PG)F_2α derivative 6 (AFP-168) has been synthesized from the Corey aldehyde in six steps. A key aspect of this route is difluorination of an enone and a stereoselective Wittig reaction. The compound shows high affinity to the FP receptor and potent activities for an anti-glaucoma agent.     

Macrocyclic lactones via biocatalysis in non-aqueous media

The enantiospecificity of lipase-catalyzed lactonization of chiral (w-1)-hydroxy acids to form diolides in non-aqueous medium was investigated.     

某些含三唑取代的苯甲酸苯甲酰甲酯衍生物的合成

以三乙胺为缚酸剂，通过苯甲酸同ω－（１Ｈ－１，２，４－三唑－１－基）－ω－溴化苯乙酮反应，合成了六种含三唑取代的苯甲酸甲酰甲酯类化合物，具有较高收率。     

四(ω-羟基聚乙氧基)-季戊四醇醚及其磺酸酯化合物的合成

报道了Cascade(树状分枝化合物)分子四方向核心四-(ω-羟基聚乙氧基)-季戊四醇醚及四-(ω-对甲苯磺酰氧聚乙氧基)-季戊四醇醚的合成,其结构经元素分析、IR、NMR和MS图谱确证。     

Growth and pectinase production by Aspergillus mexican strain protoplast regenerated under acidic stress

Protoplasts from Aspergillus sp. FP-180 and Aspergillus awamori NRRL-3112 were released and regenerated at extreme acidic conditions. The best conditions for protoplast release were 0.8 M KCI, pH 5.8, and 3h of digestion using mycelia from 12- to 16-h cultures from either Aspergillus sp. FP-180 or A. awamori NRRL-3112. The addition of fresh mycelia to an ongoing digestion after 1 h increased protoplast 4.5–5 times. A regeneration efficiency of 90% was attained at pH 6.0, and it was possible to regenerate protoplasts at pH 1.7 with a regeneration efficiency of 0.5% for Aspergillus sp. FP-180. The LpH-10 strain, derived from protoplast from Aspergillus sp FP-180, was able to regenerate at pH 1.7 and grow at pH values as low as 1.5, values at which the original strain is unable to grow. Regeneratio at extreme pH improved the performance of LpH-10 strain. It showed atwofold increase in cell growth at pH 2.0 in liquid culture and a higher pectinolytic activity in relation to that produced by the original strian.     

疏水亲脂作用驱动的有机分子的簇集和自卷

疏水亲脂相互作用(HLI)是一种重要的分子间弱作用力,本文主要介绍了HLI驱动下的有机分子分子的簇集和自卷的研究进展,作者实验室发展的一些新的概念、影响有机分子簇集和自卷的各种因素和运用这些概念对一些疾病产生原因的解释。     

一种计算无机含氧酸pk1的新公式

提出了两个新的拓扑指数：Y＝（DR＋2）／n^0.5＋2N，Z＝[(8-DR)^N(n-1)(ω-1)]^0.05。将主族元素25种单中心无机含氧酸的pκ1实验值与其Y、Z相关联，使用最小二乘法进行线性回归，拟合得：pκ1=19.977-2.430Y-0.944Z(r=0.993）。     

Photosensitivity and Physicochemical Properties of the Two-Layer Photoresist Based on Naphthoquinone Diazide and Cyclorubber

The possibility was examined of preparing a model of a two-layer photoresist based on a photo-sensitive layer of naphthoquinone diazide (FP-383), a planarizing layer of cyclorubber (FN-11), enhancing the photosensitivity and physicochemical resistance of FN-11 films after irradiation through thenaphthoquinone diazide layer and its removal by development in KOH.     

Extraction of some univalent salts into 1,2-dichloroethane and nitrobenzene: analysis of overall extraction equilibrium based on elucidating ion-pair formation and evaluation of standard potentials for ion transfers at the interfaces between their diluents and water

Sodium permanganate, sodium picrate (NaPic), Bu(4)NPic, Me(4)NPic, and Et(4)NPic were extracted at an ionic strength of 2 × 10(-5) to 0.08 mol dm(-3) and 25°C from water (w)-phases into the organic (o)-ones, 1,2-dichloroethane (DCE) and nitrobenzene (NB). Thereby, apparent distribution constants (K(D,±)) of the anions (A(-)) or the cations (M(+)) and ion-pair formation ones (K(MA)(org)) of the univalent salts (MA) in the o-phases were determined at 25 °C, where K(D,±) = ([A(-)](o)[M(+)](o)/[A(-)][M(+)])(1/2) = (K(D,A)K(D,M))(1/2) and K(MA)(org) = [MA](o)/[M(+)](o)[A(-)](o). Also, the K(ex) and K(D,MA) values with A(-) = Pic(-), MnO(4)(-) were estimated from the relations K(ex) (= [MA](o)/[M(+)][A(-)]) = K(MA)(org)(K(D,±))(2) and = K(MA)K(D,MA), respectively. Standard potentials (Δψ(tr)(0)) for ion transfers at the w/DCE and w/NB interfaces were evaluated from the log K(D,A) or log K(D,M) values by assuming the relations K(D,Pic) = K(D,Et4N) and = K(D,Me4N), respectively. The thus-obtained Δψ(tr)(0) values, especially for the w/DCE system, were in good agreement with the values based on the extra-thermodynamic assumption for Ph(4)As(+) and BPh(4)(-) transfers at the interfaces. In the present extraction systems, the ion-pair formation of MA in the w- and o-phases was less effective in the determination of their distribution constants into the two o-phases.     

Electrospray tandem mass spectrometry of mixed-sequence RNA/DNA oligonucleotides

The fragmentation of electrospray-generated multiply deprotonated RNA and mixed-sequence RNA/DNA pentanucleotides upon low-energy collision-induced dissociation (CID) in a hybrid quadrupole time-of-flight mass spectrometer was investigated. The goal of unambiguous sequence identification of mixed-sequence RNA/DNA oligonucleotides requires detailed understanding of the gas-phase dissociation of this class of compounds. The two major dissociation events, base loss and backbone fragmentation, are discussed and the unique fragmentation behavior of oligoribonucleotides is demonstrated. Backbone fragmentation of the all-RNA pentanucleotides is characterized by abundant c-ions and their complementary y-ions as the major sequence-defining fragment ion series. In contrast to the dissociation of oligodeoxyribonucleotides, where backbone fragmentation is initiated by the loss of a nucleobase which subsequently leads to the formation of the w- and [a-base]-ions, backbone dissociation of oligoribonucleotides is essentially decoupled from base loss. The different behavior of RNA and DNA oligonucleotides is related to the presence of the 2'-hydroxyl substituent, which is the only structural alteration between the DNA and RNA pentanucleotides studied. CID of mixed-sequence RNA/DNA pentanucleotides results in a combination of the nucleotide-typical backbone fragmentation products, with abundant w-fragment ions generated by cleavage of the phosphodiester backbone adjacent to the deoxy building blocks, whereas backbone cleavage adjacent to ribonucleotides induces the formation of c- and y-ions.     

1H and 13C NMR assignments of two new indolic enamide diastereomers from a mangrove endophytic fungus Aspergillus sp

Terpeptin A (1) and B (2), two new members of the indolic enamides, along with three known compounds (3-5) were identified from a strain of Aspergillus sp. (w-6), an endophytic fungus associated with Acanthus ilicifolius. The complete (1)H and (13)C NMR assignments for these compounds were carried out using (1)H, (13)C, DEPT, COSY, HMQC, and HMBC NMR experiments. Terpeptin A and B exhibited modest cytotoxicity against A-549 cell line.     

Synthesis of Polyphosphonates Containing 5—Flouro—N^1—furanyl—N^3—glyceroalkyl—uracil and Formyl Groups

A series of novel polyphosphonates containing 5-flouro-N^1-furanyl-N^3-glyceroalkyl-uracil and formyl groups was synthesized by the condensation of 3-(ω-(1′-furanyl-5-flourouracil-3-yl) alkoxy)-1,2-dihydroxy propane with phosphonyl dichloride. The products were characterized by IR,^1H NMR,^31P NMR, M,and elemental analysis. The results of bioassay show that compound 8a possesses potential anticancer activity.     

Light-Induced Reaction of Benzene with Carbonates

We found an ultraviolet (UV)-light induced formation of biphenyl and sodium benzoate from benzene and sodium carbonate. The reaction happens in the interface of benzene and aqueous solution at the room temperature. After 5 h of UV-light exposure, 11.4% of initial amount of 4.4 g (5.0 mL) benzene are converted to biphenyl and sodium benzoate, which are distributed in benzene and aqueous solution, respectively. Using density function theory (DFT) and time dependent DFT, we have investigated the mechanism of this light-induced reaction, and found that the sodium carbonate is not only a reactant for the formation of sodium benzoate, but also a catalyst for the formation of biphenyl.